diff --git a/test/data/data_mutations_extended_100.in.txt b/test/data/data_mutations_extended_100.in.txt index 941bce1e..5b7f8fa1 100644 --- a/test/data/data_mutations_extended_100.in.txt +++ b/test/data/data_mutations_extended_100.in.txt @@ -1,100 +1,100 @@ -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons -SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt -ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G P-0000004-T01-IM3 180 13 ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg -PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 225 15 ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc -MAP3K1 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G P-0000004-T01-IM3 370 12 ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt -FLT4 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A P-0000004-T01-IM3 360 25 ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg -FLT4 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C P-0000004-T01-IM3 273 22 ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg -NOTCH4 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 279 17 ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg -NOTCH4 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 207 11 ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg -MLL3 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA -MLL2 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 247 16 ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg -TSHR GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A P-0000004-T01-IM3 195 13 ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc -AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 202 244 ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag -TSC2 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 236 22 ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg -RNF43 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 296 41 ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg -NOTCH3 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 274 17 ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa -TP53 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 ENST00000269305.4:c.412_427delGCCAAGACCTGCCCTG p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg -ALK GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A P-0000015-T01-IM3 80 56 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag -ESR1 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc -CDK4 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A P-0000015-T01-IM3 131 61 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg -RNF43 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg -GATA3 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 ENST00000346208.3:c.1003dupG p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G -LATS1 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc -LATS1 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A P-0000023-T01-IM3 511 38 ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga -U2AF1 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc -BAP1 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 ENST00000460680.1:c.983delC p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct -LATS2 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 ENST00000382592.4:c.2538dupT p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T -CTNNB1 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A P-0000024-T01-IM3 965 280 ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt -PTEN GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G P-0000024-T01-IM3 846 231 ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga -BCOR GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C P-0000024-T01-IM3 647 317 ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt -ARID1A GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 ENST00000324856.7:c.5489_5492delAGCT p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at -PIK3R1 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 ENST00000521381.1:c.1746-8_1748delTTTTTCAGGTG p.X582_splice ENST00000521381 NM_181523.2 -PTEN GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A P-0000024-T01-IM3 170 53 ENST00000371953.3:c.875dupA p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T P-0000025-T01-IM3 827 49 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T P-0000026-T01-IM3 261 370 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg -PIK3CA GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A P-0000026-T01-IM3 325 468 ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag -LATS1 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct -IKZF1 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A P-0000027-T01-IM3 122 16 ENST00000310581 NM_198253.2 -CUL3 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat -ABL1 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc -MYCL1 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt -POLE GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG -TP53 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A P-0000037-T01-IM3 293 230 ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT -NCOR1 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att -ARID1A GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa -RYBP GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 ENST00000477973.2:c.938G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat -FAT1 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A P-0000034-T01-IM3 659 78 ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga -FGFR4 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat -BLM GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag -BLM GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T P-0000034-T01-IM3 631 51 ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa -BLM GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa -BLM GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc -BLM GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG -BLM GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac -CIC GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A P-0000034-T01-IM3 217 76 ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg -KDM6A GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 ENST00000377967.4:c.4108delG p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt -FOXP1 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt -AKT1 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C P-0000047-T01-IM3 220 25 ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt -BAP1 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 ENST00000460680.1:c.100_118delGACCTTCAGAGCAAATGTC p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag -TP53 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 698 390 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt -NRAS GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA -ATR GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt -PIK3CA GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 935 227 ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa -NOTCH3 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag -PIK3R1 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 ENST00000521381.1:c.1344dupA p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A P-0000056-T01-IM3 271 161 ENST00000310581 NM_198253.2 -BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A P-0000056-T01-IM3 617 328 ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc -FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca -NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc -CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T P-0000056-T01-IM3 1248 88 ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag -FGFR3 37 4 1806090 1806090 In_Frame_Ins DEL A A CACT P-0000056-T01-IM3 816 370 -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A P-0000057-T01-IM3 389 132 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag -BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa -MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt -NOTCH4 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag -TP53 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A P-0000057-T01-IM3 442 261 ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga -TP53 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G P-0000058-T01-IM3 156 348 ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T P-0000060-T01-IM3 162 217 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg -PIK3CA GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G P-0000060-T01-IM3 779 359 ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt -PTEN GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt -BRCA2 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A P-0000060-T01-IM3 293 148 ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa -SMO GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 ENST00000249373.3:c.1943delC p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc -MCL1 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 ENST00000369026.2:c.626_643delCGCTGGAGACCTTACGACinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg -PIK3CA GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C P-0000061-T01-IM3 762 155 ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt -FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac -SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A P-0000062-T01-IM3 265 581 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg -EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A P-0000062-T01-IM3 980 54 ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg -MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg -IGF1R GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG -KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 807 422 ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG -KDM5C GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A P-0000063-T01-IM3 18 79 ENST00000310581 NM_198253.2 -EPHB1 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T P-0000063-T01-IM3 540 220 ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag -FGFR3 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc -FAT1 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac -FAT1 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Hotspot +SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 0 +ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G P-0000004-T01-IM3 180 13 ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 0 +PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 225 15 ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 0 +MAP3K1 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G P-0000004-T01-IM3 370 12 ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 0 +FLT4 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A P-0000004-T01-IM3 360 25 ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 0 +FLT4 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C P-0000004-T01-IM3 273 22 ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 0 +NOTCH4 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 279 17 ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 0 +NOTCH4 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 207 11 ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 0 +MLL3 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 0 +MLL2 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 247 16 ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 0 +TSHR GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A P-0000004-T01-IM3 195 13 ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 0 +AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 202 244 ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 0 +TSC2 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 236 22 ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 0 +RNF43 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A P-0000004-T01-IM3 296 41 ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 0 +NOTCH3 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 274 17 ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 0 +TP53 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 ENST00000269305.4:c.412_427delGCCAAGACCTGCCCTG p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 0 +ALK GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 0 +PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A P-0000015-T01-IM3 80 56 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 0 +ESR1 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 0 +CDK4 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 0 +TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A P-0000015-T01-IM3 131 61 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 0 +RNF43 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 0 +GATA3 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 ENST00000346208.3:c.1003dupG p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 0 +LATS1 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 0 +LATS1 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A P-0000023-T01-IM3 511 38 ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 0 +U2AF1 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 0 +BAP1 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 ENST00000460680.1:c.983delC p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 0 +LATS2 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 ENST00000382592.4:c.2538dupT p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 0 +CTNNB1 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A P-0000024-T01-IM3 965 280 ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 0 +PTEN GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G P-0000024-T01-IM3 846 231 ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 0 +BCOR GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C P-0000024-T01-IM3 647 317 ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 0 +ARID1A GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 ENST00000324856.7:c.5489_5492delAGCT p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 0 +PIK3R1 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 ENST00000521381.1:c.1746-8_1748delTTTTTCAGGTG p.X582_splice ENST00000521381 NM_181523.2 0 +PTEN GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A P-0000024-T01-IM3 170 53 ENST00000371953.3:c.875dupA p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 0 +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T P-0000025-T01-IM3 827 49 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 0 +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T P-0000026-T01-IM3 261 370 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 0 +PIK3CA GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A P-0000026-T01-IM3 325 468 ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 0 +LATS1 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 0 +IKZF1 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 0 +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A P-0000027-T01-IM3 122 16 ENST00000310581 NM_198253.2 0 +CUL3 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 0 +ABL1 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 0 +MYCL1 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 0 +POLE GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 0 +TP53 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A P-0000037-T01-IM3 293 230 ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 0 +NCOR1 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 0 +ARID1A GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 0 +RYBP GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 ENST00000477973.2:c.938G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 0 +FAT1 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A P-0000034-T01-IM3 659 78 ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 0 +FGFR4 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 0 +BLM GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 0 +BLM GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T P-0000034-T01-IM3 631 51 ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 0 +BLM GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 0 +BLM GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 0 +BLM GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 0 +BLM GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 0 +CIC GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A P-0000034-T01-IM3 217 76 ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 0 +KDM6A GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 ENST00000377967.4:c.4108delG p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 0 +FOXP1 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 0 +AKT1 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C P-0000047-T01-IM3 220 25 ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 0 +BAP1 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 ENST00000460680.1:c.100_118delGACCTTCAGAGCAAATGTC p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 0 +TP53 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 698 390 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 0 +NRAS GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 0 +ATR GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 0 +PIK3CA GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 935 227 ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 0 +NOTCH3 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 0 +PIK3R1 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 ENST00000521381.1:c.1344dupA p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 0 +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A P-0000056-T01-IM3 271 161 ENST00000310581 NM_198253.2 0 +BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A P-0000056-T01-IM3 617 328 ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 0 +FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 0 +NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 0 +CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T P-0000056-T01-IM3 1248 88 ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 0 +FGFR3 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G A CACT P-0000056-T01-IM3 816 370 ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 0 +PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A P-0000057-T01-IM3 389 132 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 0 +BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 0 +MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 0 +NOTCH4 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 0 +TP53 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A P-0000057-T01-IM3 442 261 ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 0 +TP53 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G P-0000058-T01-IM3 156 348 ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 0 +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T P-0000060-T01-IM3 162 217 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 0 +PIK3CA GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G P-0000060-T01-IM3 779 359 ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 0 +PTEN GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 0 +BRCA2 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A P-0000060-T01-IM3 293 148 ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 0 +SMO GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 ENST00000249373.3:c.1943delC p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 0 +MCL1 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 ENST00000369026.2:c.626_643delCGCTGGAGACCTTACGACinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 0 +PIK3CA GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C P-0000061-T01-IM3 762 155 ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 0 +FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 0 +SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 0 +TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A P-0000062-T01-IM3 265 581 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 0 +EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A P-0000062-T01-IM3 980 54 ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 0 +MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 0 +IGF1R GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 0 +KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 807 422 ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 0 +KDM5C GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 0 +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A P-0000063-T01-IM3 18 79 ENST00000310581 NM_198253.2 0 +EPHB1 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T P-0000063-T01-IM3 540 220 ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 0 +FGFR3 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 0 +FAT1 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 0 +FAT1 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 0 diff --git a/test/data/data_mutations_extended_100.out.mskcc.txt b/test/data/data_mutations_extended_100.out.mskcc.txt index c90ad22d..c371fc2b 100644 --- a/test/data/data_mutations_extended_100.out.mskcc.txt +++ b/test/data/data_mutations_extended_100.out.mskcc.txt @@ -1,102 +1,102 @@ #genome_nexus_version: 0-unknown-version-SNAPSHOT #isoform: mskcc -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS -ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 SUCCESS -PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 SUCCESS -MAP3K1 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 SUCCESS -FLT4 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 SUCCESS -FLT4 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 SUCCESS -NOTCH4 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 SUCCESS -NOTCH4 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 SUCCESS -MLL3 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS -MLL2 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS -TSHR GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 ENST00000298171.2:c.154C>A p.Pro52Thr p.P52T ENST00000298171 NM_000369.2 52 Ccc/Acc 1/10 SUCCESS -AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 SUCCESS -TSC2 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 SUCCESS -RNF43 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 SUCCESS -NOTCH3 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 SUCCESS -TP53 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS -ALK GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 SUCCESS -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS -ESR1 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 SUCCESS -CDK4 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 SUCCESS -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS -RNF43 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 SUCCESS -GATA3 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS -LATS1 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 SUCCESS -LATS1 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 SUCCESS -U2AF1 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 SUCCESS -BAP1 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS -LATS2 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS -CTNNB1 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 SUCCESS -PTEN GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 SUCCESS -BCOR GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 SUCCESS -ARID1A GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS -PIK3R1 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 ENST00000274335.5:c.1746-8_1748del p.X582_splice ENST00000274335 582 13/15 SUCCESS -PTEN GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -PIK3CA GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 SUCCESS -LATS1 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 SUCCESS -IKZF1 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 ENST00000310581 NM_198253.2 SUCCESS -CUL3 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 SUCCESS -ABL1 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 SUCCESS -MYCL1 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 ENST00000397332.2:c.851T>G p.Ile284Ser p.I284S ENST00000397332 NM_001033082.2 284 aTt/aGt 3/3 SUCCESS -POLE GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 SUCCESS -TP53 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 SUCCESS -NCOR1 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 SUCCESS -ARID1A GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 SUCCESS -RYBP GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 SUCCESS -FAT1 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 SUCCESS -FGFR4 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 SUCCESS -BLM GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 SUCCESS -BLM GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 SUCCESS -BLM GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 SUCCESS -BLM GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 SUCCESS -BLM GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 SUCCESS -BLM GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 SUCCESS -CIC GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 SUCCESS -KDM6A GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS -FOXP1 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 SUCCESS -AKT1 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 SUCCESS -BAP1 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS -TP53 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 SUCCESS -NRAS GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 SUCCESS -ATR GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 SUCCESS -PIK3CA GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 SUCCESS -NOTCH3 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 SUCCESS -PIK3R1 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 ENST00000274335.5:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000274335 446 -/A 10/15 SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 ENST00000310581 NM_198253.2 SUCCESS -BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 SUCCESS -FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 SUCCESS -NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS -CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 SUCCESS -FGFR3 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS -BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 SUCCESS -MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS -NOTCH4 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 SUCCESS -TP53 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 SUCCESS -TP53 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -PIK3CA GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 SUCCESS -PTEN GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 SUCCESS -BRCA2 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 SUCCESS -SMO GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS -MCL1 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS -PIK3CA GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 SUCCESS -FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 SUCCESS -SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 SUCCESS -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS -EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 ENST00000320356.2:c.848C>T p.Thr283Met p.T283M ENST00000320356 NM_004456.4 283 aCg/aTg 8/20 SUCCESS -MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 SUCCESS -IGF1R GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 SUCCESS -KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 SUCCESS -KDM5C GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 ENST00000310581 NM_198253.2 SUCCESS -EPHB1 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 SUCCESS -FGFR3 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 SUCCESS -FAT1 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 SUCCESS -FAT1 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Hotspot Annotation_Status +SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 0 SUCCESS +ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 0 SUCCESS +PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 0 SUCCESS +MAP3K1 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 0 SUCCESS +FLT4 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 0 SUCCESS +FLT4 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 0 SUCCESS +NOTCH4 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 0 SUCCESS +NOTCH4 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 0 SUCCESS +MLL3 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 0 SUCCESS +MLL2 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 0 SUCCESS +TSHR GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 ENST00000298171.2:c.154C>A p.Pro52Thr p.P52T ENST00000298171 NM_000369.2 52 Ccc/Acc 1/10 0 SUCCESS +AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 0 SUCCESS +TSC2 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 0 SUCCESS +RNF43 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 0 SUCCESS +NOTCH3 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 0 SUCCESS +TP53 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 0 SUCCESS +ALK GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 0 SUCCESS +PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 0 SUCCESS +ESR1 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 0 SUCCESS +CDK4 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 0 SUCCESS +TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 0 SUCCESS +RNF43 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 0 SUCCESS +GATA3 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 0 SUCCESS +LATS1 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 0 SUCCESS +LATS1 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 0 SUCCESS +U2AF1 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 0 SUCCESS +BAP1 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 0 SUCCESS +LATS2 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 0 SUCCESS +CTNNB1 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 0 SUCCESS +PTEN GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 0 SUCCESS +BCOR GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 0 SUCCESS +ARID1A GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 0 SUCCESS +PIK3R1 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 ENST00000274335.5:c.1746-8_1748del p.X582_splice ENST00000274335 582 13/15 0 SUCCESS +PTEN GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 0 SUCCESS +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 0 SUCCESS +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 0 SUCCESS +PIK3CA GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 0 SUCCESS +LATS1 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 0 SUCCESS +IKZF1 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 0 SUCCESS +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 ENST00000310581 NM_198253.2 0 SUCCESS +CUL3 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 0 SUCCESS +ABL1 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 0 SUCCESS +MYCL1 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 ENST00000397332.2:c.851T>G p.Ile284Ser p.I284S ENST00000397332 NM_001033082.2 284 aTt/aGt 3/3 0 SUCCESS +POLE GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 0 SUCCESS +TP53 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 0 SUCCESS +NCOR1 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 0 SUCCESS +ARID1A GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 0 SUCCESS +RYBP GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 0 SUCCESS +FAT1 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 0 SUCCESS +FGFR4 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 0 SUCCESS +BLM GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 0 SUCCESS +BLM GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 0 SUCCESS +BLM GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 0 SUCCESS +BLM GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 0 SUCCESS +BLM GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 0 SUCCESS +BLM GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 0 SUCCESS +CIC GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 0 SUCCESS +KDM6A GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 0 SUCCESS +FOXP1 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 0 SUCCESS +AKT1 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 0 SUCCESS +BAP1 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 0 SUCCESS +TP53 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 0 SUCCESS +NRAS GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 0 SUCCESS +ATR GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 0 SUCCESS +PIK3CA GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 0 SUCCESS +NOTCH3 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 0 SUCCESS +PIK3R1 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 ENST00000274335.5:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000274335 446 -/A 10/15 0 SUCCESS +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 ENST00000310581 NM_198253.2 0 SUCCESS +BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 0 SUCCESS +FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 0 SUCCESS +NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 0 SUCCESS +CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 0 SUCCESS +FGFR3 GRCh37 4 1806090 1806090 + missense_variant Missense_Mutation SNP G A A P-0000056-T01-IM3 816 370 ENST00000260795.2:c.1109G>A p.Gly370Asp p.G370D ENST00000260795 370 gGc/gAc 8/17 0 SUCCESS +PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 0 SUCCESS +BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 0 SUCCESS +MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 0 SUCCESS +NOTCH4 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 0 SUCCESS +TP53 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 0 SUCCESS +TP53 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 0 SUCCESS +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 0 SUCCESS +PIK3CA GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 0 SUCCESS +PTEN GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 0 SUCCESS +BRCA2 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 0 SUCCESS +SMO GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 0 SUCCESS +MCL1 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 0 SUCCESS +PIK3CA GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 0 SUCCESS +FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 0 SUCCESS +SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 0 SUCCESS +TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 0 SUCCESS +EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 ENST00000320356.2:c.848C>T p.Thr283Met p.T283M ENST00000320356 NM_004456.4 283 aCg/aTg 8/20 0 SUCCESS +MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 0 SUCCESS +IGF1R GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 0 SUCCESS +KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 0 SUCCESS +KDM5C GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 0 SUCCESS +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 ENST00000310581 NM_198253.2 0 SUCCESS +EPHB1 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 0 SUCCESS +FGFR3 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 0 SUCCESS +FAT1 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 0 SUCCESS +FAT1 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 0 SUCCESS diff --git a/test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt b/test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt index 6df872be..dda10401 100644 --- a/test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt +++ b/test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt @@ -1,102 +1,102 @@ #genome_nexus_version: 0-unknown-version-SNAPSHOT #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Ref_Tri Var_Tri Annotation_Status -SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 CAT CTT SUCCESS -ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 CAC CGC SUCCESS -PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 GGC GAC SUCCESS -MAP3K1 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 TCT TGT SUCCESS -FLT4 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 CCG CAG SUCCESS -FLT4 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 GTG GCG SUCCESS -NOTCH4 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 CCG CTG SUCCESS -NOTCH4 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 CGA CAA SUCCESS -MLL3 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 GCA GTA SUCCESS -MLL2 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 CGG CAG SUCCESS -TSHR GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 2/11 GCC GAC SUCCESS -AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 TCC TTC SUCCESS -TSC2 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 CGG CAG SUCCESS -RNF43 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 CGG CAG SUCCESS -NOTCH3 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 TCG TTG SUCCESS -TP53 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS -ALK GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 GCC GTC SUCCESS -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 TGA TAA SUCCESS -ESR1 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 CTC CAC SUCCESS -CDK4 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 TCC TGC SUCCESS -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 CGG CAG SUCCESS -RNF43 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 CCA CGA SUCCESS -GATA3 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS -LATS1 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 GTC GAC SUCCESS -LATS1 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 CGA CAA SUCCESS -U2AF1 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 GTT GCT SUCCESS -BAP1 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS -LATS2 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS -CTNNB1 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 TCT TAT SUCCESS -PTEN GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 ACG AGG SUCCESS -BCOR GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 ATT ACT SUCCESS -ARID1A GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS -PIK3R1 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 ENST00000521381.1:c.1746-8_1748del p.X582_splice ENST00000521381 NM_181523.2 582 14/16 SUCCESS -PTEN GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A P-0000024-T01-IM3 170 53 ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 CCG CTG SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 CCG CTG SUCCESS -PIK3CA GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 GCA GAA SUCCESS -LATS1 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 GGG GCG SUCCESS -IKZF1 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 CGC CAC SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 ENST00000310581 NM_198253.2 AGG AAG SUCCESS -CUL3 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 TAT TGT SUCCESS -ABL1 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 TGC TAC SUCCESS -MYCL1 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2/2 AAT ACT SUCCESS -POLE GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 GGT GCT SUCCESS -TP53 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 GCC GAC SUCCESS -NCOR1 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 AGA ATA SUCCESS -ARID1A GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 TCA TGA SUCCESS -RYBP GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 ENST00000477973.2:c.938G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 TCA TGA SUCCESS -FAT1 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 CGA CAA SUCCESS -FGFR4 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 AGA ACA SUCCESS -BLM GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 TCA TTA SUCCESS -BLM GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 TCA TTA SUCCESS -BLM GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 TCA TAA SUCCESS -BLM GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 TCT TGT SUCCESS -BLM GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 TCA TGA SUCCESS -BLM GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 TCA TGA SUCCESS -CIC GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 CGT CAT SUCCESS -KDM6A GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS -FOXP1 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 CTT CCT SUCCESS -AKT1 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 ATA ACA SUCCESS -BAP1 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS -TP53 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 ACG ATG SUCCESS -NRAS GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 TCA TTA SUCCESS -ATR GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 AGA AAA SUCCESS -PIK3CA GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 AGA AAA SUCCESS -NOTCH3 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 TCC TTC SUCCESS -PIK3R1 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 11/16 SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 ENST00000310581 NM_198253.2 AGG AAG SUCCESS -BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 CGC CAC SUCCESS -FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 GGC GTC SUCCESS -NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 GTA GCA SUCCESS -CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 GGA GTA SUCCESS -FGFR3 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 TGA TAA SUCCESS -BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 TGT TCT SUCCESS -MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 TCT TTT SUCCESS -NOTCH4 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 TCG TGG SUCCESS -TP53 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 CGG CAG SUCCESS -TP53 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 GAT GGT SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 CCG CTG SUCCESS -PIK3CA GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 CAT CGT SUCCESS -PTEN GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 GTT GCT SUCCESS -BRCA2 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 AGG AAG SUCCESS -SMO GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS -MCL1 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS -PIK3CA GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 TGG TCG SUCCESS -FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 TCA TGA SUCCESS -SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 GCG GGG SUCCESS -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 CGG CAG SUCCESS -EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 8/20 CGT CAT SUCCESS -MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 GAG GTG SUCCESS -IGF1R GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 ATT AGT SUCCESS -KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 AGA ACA SUCCESS -KDM5C GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 GGA GCA SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 ENST00000310581 NM_198253.2 AGG AAG SUCCESS -EPHB1 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 CCA CTA SUCCESS -FGFR3 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 TCC TTC SUCCESS -FAT1 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 TCA TGA SUCCESS -FAT1 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 TCT TGT SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Hotspot Ref_Tri Var_Tri Annotation_Status +SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 0 CAT CTT SUCCESS +ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 0 CAC CGC SUCCESS +PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 0 GGC GAC SUCCESS +MAP3K1 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 0 TCT TGT SUCCESS +FLT4 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 0 CCG CAG SUCCESS +FLT4 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 0 GTG GCG SUCCESS +NOTCH4 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 0 CCG CTG SUCCESS +NOTCH4 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 0 CGA CAA SUCCESS +MLL3 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 0 GCA GTA SUCCESS +MLL2 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 0 CGG CAG SUCCESS +TSHR GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 2/11 0 GCC GAC SUCCESS +AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 0 TCC TTC SUCCESS +TSC2 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 0 CGG CAG SUCCESS +RNF43 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 0 CGG CAG SUCCESS +NOTCH3 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 0 TCG TTG SUCCESS +TP53 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 0 SUCCESS +ALK GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 0 GCC GTC SUCCESS +PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 0 TGA TAA SUCCESS +ESR1 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 0 CTC CAC SUCCESS +CDK4 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 0 TCC TGC SUCCESS +TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 0 CGG CAG SUCCESS +RNF43 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 0 CCA CGA SUCCESS +GATA3 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 0 SUCCESS +LATS1 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 0 GTC GAC SUCCESS +LATS1 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 0 CGA CAA SUCCESS +U2AF1 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 0 GTT GCT SUCCESS +BAP1 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 0 SUCCESS +LATS2 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 0 SUCCESS +CTNNB1 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 0 TCT TAT SUCCESS +PTEN GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 0 ACG AGG SUCCESS +BCOR GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 0 ATT ACT SUCCESS +ARID1A GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 0 SUCCESS +PIK3R1 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 ENST00000521381.1:c.1746-8_1748del p.X582_splice ENST00000521381 NM_181523.2 582 14/16 0 SUCCESS +PTEN GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 0 SUCCESS +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 0 CCG CTG SUCCESS +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 0 CCG CTG SUCCESS +PIK3CA GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 0 GCA GAA SUCCESS +LATS1 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 0 GGG GCG SUCCESS +IKZF1 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 0 CGC CAC SUCCESS +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 ENST00000310581 NM_198253.2 0 AGG AAG SUCCESS +CUL3 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 0 TAT TGT SUCCESS +ABL1 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 0 TGC TAC SUCCESS +MYCL1 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2/2 0 AAT ACT SUCCESS +POLE GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 0 GGT GCT SUCCESS +TP53 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 0 GCC GAC SUCCESS +NCOR1 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 0 AGA ATA SUCCESS +ARID1A GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 0 TCA TGA SUCCESS +RYBP GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 0 TCA TGA SUCCESS +FAT1 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 0 CGA CAA SUCCESS +FGFR4 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 0 AGA ACA SUCCESS +BLM GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 0 TCA TTA SUCCESS +BLM GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 0 TCA TTA SUCCESS +BLM GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 0 TCA TAA SUCCESS +BLM GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 0 TCT TGT SUCCESS +BLM GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 0 TCA TGA SUCCESS +BLM GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 0 TCA TGA SUCCESS +CIC GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 0 CGT CAT SUCCESS +KDM6A GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 0 SUCCESS +FOXP1 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 0 CTT CCT SUCCESS +AKT1 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 0 ATA ACA SUCCESS +BAP1 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 0 SUCCESS +TP53 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 0 ACG ATG SUCCESS +NRAS GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 0 TCA TTA SUCCESS +ATR GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 0 AGA AAA SUCCESS +PIK3CA GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 0 AGA AAA SUCCESS +NOTCH3 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 0 TCC TTC SUCCESS +PIK3R1 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 11/16 0 SUCCESS +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 ENST00000310581 NM_198253.2 0 AGG AAG SUCCESS +BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 0 CGC CAC SUCCESS +FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 0 GGC GTC SUCCESS +NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 0 GTA GCA SUCCESS +CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 0 GGA GTA SUCCESS +FGFR3 GRCh37 4 1806090 1806090 + missense_variant Missense_Mutation SNP G A A P-0000056-T01-IM3 816 370 ENST00000260795.2:c.1109G>A p.Gly370Asp p.G370D ENST00000260795 370 gGc/gAc 8/17 0 GGC GAC SUCCESS +PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 0 TGA TAA SUCCESS +BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 0 TGT TCT SUCCESS +MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 0 TCT TTT SUCCESS +NOTCH4 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 0 TCG TGG SUCCESS +TP53 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 0 CGG CAG SUCCESS +TP53 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 0 GAT GGT SUCCESS +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 0 CCG CTG SUCCESS +PIK3CA GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 0 CAT CGT SUCCESS +PTEN GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 0 GTT GCT SUCCESS +BRCA2 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 0 AGG AAG SUCCESS +SMO GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 0 SUCCESS +MCL1 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 0 SUCCESS +PIK3CA GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 0 TGG TCG SUCCESS +FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 0 TCA TGA SUCCESS +SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 0 GCG GGG SUCCESS +TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 0 CGG CAG SUCCESS +EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 8/20 0 CGT CAT SUCCESS +MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 0 GAG GTG SUCCESS +IGF1R GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 0 ATT AGT SUCCESS +KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 0 AGA ACA SUCCESS +KDM5C GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 0 GGA GCA SUCCESS +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 ENST00000310581 NM_198253.2 0 AGG AAG SUCCESS +EPHB1 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 0 CCA CTA SUCCESS +FGFR3 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 0 TCC TTC SUCCESS +FAT1 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 0 TCA TGA SUCCESS +FAT1 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 0 TCT TGT SUCCESS diff --git a/test/data/data_mutations_extended_100.out.uniprot.txt b/test/data/data_mutations_extended_100.out.uniprot.txt index a8482108..53538e4b 100644 --- a/test/data/data_mutations_extended_100.out.uniprot.txt +++ b/test/data/data_mutations_extended_100.out.uniprot.txt @@ -1,102 +1,102 @@ #genome_nexus_version: 0-unknown-version-SNAPSHOT #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS -ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 SUCCESS -PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 SUCCESS -MAP3K1 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 SUCCESS -FLT4 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 SUCCESS -FLT4 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 SUCCESS -NOTCH4 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 SUCCESS -NOTCH4 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 SUCCESS -MLL3 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS -MLL2 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS -TSHR GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 2/11 SUCCESS -AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 SUCCESS -TSC2 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 SUCCESS -RNF43 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 SUCCESS -NOTCH3 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 SUCCESS -TP53 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS -ALK GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 SUCCESS -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS -ESR1 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 SUCCESS -CDK4 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 SUCCESS -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS -RNF43 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 SUCCESS -GATA3 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS -LATS1 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 SUCCESS -LATS1 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 SUCCESS -U2AF1 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 SUCCESS -BAP1 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS -LATS2 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS -CTNNB1 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 SUCCESS -PTEN GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 SUCCESS -BCOR GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 SUCCESS -ARID1A GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS -PIK3R1 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 ENST00000521381.1:c.1746-8_1748del p.X582_splice ENST00000521381 NM_181523.2 582 14/16 SUCCESS -PTEN GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -PIK3CA GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 SUCCESS -LATS1 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 SUCCESS -IKZF1 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 ENST00000310581 NM_198253.2 SUCCESS -CUL3 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 SUCCESS -ABL1 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 SUCCESS -MYCL1 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2/2 SUCCESS -POLE GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 SUCCESS -TP53 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 SUCCESS -NCOR1 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 SUCCESS -ARID1A GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 SUCCESS -RYBP GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 SUCCESS -FAT1 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 SUCCESS -FGFR4 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 SUCCESS -BLM GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 SUCCESS -BLM GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 SUCCESS -BLM GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 SUCCESS -BLM GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 SUCCESS -BLM GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 SUCCESS -BLM GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 SUCCESS -CIC GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 SUCCESS -KDM6A GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS -FOXP1 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 SUCCESS -AKT1 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 SUCCESS -BAP1 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS -TP53 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 SUCCESS -NRAS GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 SUCCESS -ATR GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 SUCCESS -PIK3CA GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 SUCCESS -NOTCH3 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 SUCCESS -PIK3R1 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 11/16 SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 ENST00000310581 NM_198253.2 SUCCESS -BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 SUCCESS -FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 SUCCESS -NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS -CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 SUCCESS -FGFR3 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS -BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 SUCCESS -MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS -NOTCH4 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 SUCCESS -TP53 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 SUCCESS -TP53 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -PIK3CA GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 SUCCESS -PTEN GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 SUCCESS -BRCA2 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 SUCCESS -SMO GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS -MCL1 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS -PIK3CA GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 SUCCESS -FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 SUCCESS -SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 SUCCESS -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS -EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 8/20 SUCCESS -MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 SUCCESS -IGF1R GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 SUCCESS -KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 SUCCESS -KDM5C GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 ENST00000310581 NM_198253.2 SUCCESS -EPHB1 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 SUCCESS -FGFR3 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 SUCCESS -FAT1 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 SUCCESS -FAT1 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Hotspot Annotation_Status +SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 0 SUCCESS +ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 0 SUCCESS +PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 0 SUCCESS +MAP3K1 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 0 SUCCESS +FLT4 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 0 SUCCESS +FLT4 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 0 SUCCESS +NOTCH4 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 0 SUCCESS +NOTCH4 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 0 SUCCESS +MLL3 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 0 SUCCESS +MLL2 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 0 SUCCESS +TSHR GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 2/11 0 SUCCESS +AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 0 SUCCESS +TSC2 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 0 SUCCESS +RNF43 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 0 SUCCESS +NOTCH3 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 0 SUCCESS +TP53 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 0 SUCCESS +ALK GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 0 SUCCESS +PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 0 SUCCESS +ESR1 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 0 SUCCESS +CDK4 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 0 SUCCESS +TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 0 SUCCESS +RNF43 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 0 SUCCESS +GATA3 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 0 SUCCESS +LATS1 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 0 SUCCESS +LATS1 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 0 SUCCESS +U2AF1 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 0 SUCCESS +BAP1 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 0 SUCCESS +LATS2 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 0 SUCCESS +CTNNB1 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 0 SUCCESS +PTEN GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 0 SUCCESS +BCOR GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 0 SUCCESS +ARID1A GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 0 SUCCESS +PIK3R1 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 ENST00000521381.1:c.1746-8_1748del p.X582_splice ENST00000521381 NM_181523.2 582 14/16 0 SUCCESS +PTEN GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 0 SUCCESS +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 0 SUCCESS +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 0 SUCCESS +PIK3CA GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 0 SUCCESS +LATS1 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 0 SUCCESS +IKZF1 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 0 SUCCESS +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 ENST00000310581 NM_198253.2 0 SUCCESS +CUL3 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 0 SUCCESS +ABL1 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 0 SUCCESS +MYCL1 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2/2 0 SUCCESS +POLE GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 0 SUCCESS +TP53 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 0 SUCCESS +NCOR1 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 0 SUCCESS +ARID1A GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 0 SUCCESS +RYBP GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 0 SUCCESS +FAT1 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 0 SUCCESS +FGFR4 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 0 SUCCESS +BLM GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 0 SUCCESS +BLM GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 0 SUCCESS +BLM GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 0 SUCCESS +BLM GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 0 SUCCESS +BLM GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 0 SUCCESS +BLM GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 0 SUCCESS +CIC GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 0 SUCCESS +KDM6A GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 0 SUCCESS +FOXP1 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 0 SUCCESS +AKT1 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 0 SUCCESS +BAP1 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 0 SUCCESS +TP53 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 0 SUCCESS +NRAS GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 0 SUCCESS +ATR GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 0 SUCCESS +PIK3CA GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 0 SUCCESS +NOTCH3 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 0 SUCCESS +PIK3R1 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 11/16 0 SUCCESS +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 ENST00000310581 NM_198253.2 0 SUCCESS +BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 0 SUCCESS +FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 0 SUCCESS +NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 0 SUCCESS +CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 0 SUCCESS +FGFR3 GRCh37 4 1806090 1806090 + missense_variant Missense_Mutation SNP G A A P-0000056-T01-IM3 816 370 ENST00000260795.2:c.1109G>A p.Gly370Asp p.G370D ENST00000260795 370 gGc/gAc 8/17 0 SUCCESS +PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 0 SUCCESS +BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 0 SUCCESS +MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 0 SUCCESS +NOTCH4 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 0 SUCCESS +TP53 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 0 SUCCESS +TP53 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 0 SUCCESS +TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 0 SUCCESS +PIK3CA GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 0 SUCCESS +PTEN GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 0 SUCCESS +BRCA2 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 0 SUCCESS +SMO GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 0 SUCCESS +MCL1 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 0 SUCCESS +PIK3CA GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 0 SUCCESS +FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 0 SUCCESS +SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 0 SUCCESS +TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 0 SUCCESS +EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 8/20 0 SUCCESS +MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 0 SUCCESS +IGF1R GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 0 SUCCESS +KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 0 SUCCESS +KDM5C GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 0 SUCCESS +TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 ENST00000310581 NM_198253.2 0 SUCCESS +EPHB1 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 0 SUCCESS +FGFR3 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 0 SUCCESS +FAT1 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 0 SUCCESS +FAT1 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 0 SUCCESS