diff --git a/notebooks/AMT/AMT_GCE2_individuals.ipynb b/notebooks/AMT/AMT_GCE2_individuals.ipynb new file mode 100644 index 00000000..9e8f891f --- /dev/null +++ b/notebooks/AMT/AMT_GCE2_individuals.ipynb @@ -0,0 +1,160 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# AMT\n", + "[glycine encephalopathy-2 (GCE2)](https://omim.org/entry/620398) is caused by homozygous or compound heterozygous mutation in the AMT gene." + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Using pyphetools version 0.9.115\n" + ] + } + ], + "source": [ + "from pyphetools.creation import TemplateImporter, Moi\n", + "from pyphetools.visualization import IndividualTable, QcVisualizer\n", + "from IPython.display import display, HTML\n", + "import pyphetools\n", + "print(f\"Using pyphetools version {pyphetools.__version__}\")" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "HPO version 2024-12-12\n", + "Created encoders for 38 fields\n", + "Importing OMIM:620398, Glycine encephalopathy 2, HGNC:473, AMT, NM_000481.4\n", + "We output 5 GA4GH phenopackets to the directory phenopackets\n" + ] + } + ], + "source": [ + "template = \"input/AMT_GCE2_individuals.xlsx\"\n", + "created_by = \"0000-0002-0736-9199\"\n", + "deletions = {\"DEL:Total AMT gene deletion\"}\n", + "timporter = TemplateImporter(template=template, created_by=created_by)\n", + "individual_list, cvalidator = timporter.import_phenopackets_from_template(deletions=deletions)" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "

Cohort validation

\n", + "

No errors found for the cohort with 5 individuals

" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "qc = QcVisualizer(cohort_validator=cvalidator)\n", + "display(HTML(qc.to_summary_html()))" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "
5 phenopackets - PMID:8005589 (n=2); PMID:9600239 (n=1); PMID:33791923 (n=2)
IndividualDiseaseGenotypePhenotypic features
patient A (FEMALE; P19Y)Glycine encephalopathy 2 (OMIM:620398)NM_000481.4:c.806G>A (homozygous)Global developmental delay (HP:0001263): onset ; Hyperglycinuria (HP:0003108): onset ; Intellectual disability, severe (HP:0010864): onset
patient B (FEMALE; P9Y)Glycine encephalopathy 2 (OMIM:620398)
  • NM_000481.4:c.139G>A (heterozygous)
  • NM_000481.4:c.959G>A (heterozygous)
Global developmental delay (HP:0001263): onset ; Seizure (HP:0001250): onset ; Cerebral atrophy (HP:0002059): onset ; Hyperglycinuria (HP:0003108): onset ; Intellectual disability, severe (HP:0010864): onset
propositus VII-7 (MALE; P2D)Glycine encephalopathy 2 (OMIM:620398)NM_000481.4:c.125A>G (homozygous)EEG with burst suppression (HP:0010851): onset ; Increased CSF glycine concentration (HP:0500230): onset ; Hyperglycinemia (HP:0002154): onset
TimeElement(element=Age(iso8601duration=P2D)): Seizure (HP:0001250): onset age {\n", + " iso8601duration: \"P2D\"\n", + "}\n", + "
Patient 6 (FEMALE; P5D)Glycine encephalopathy 2 (OMIM:620398)NM_000481.4:c.434A>T (homozygous)Global developmental delay (HP:0001263): onset ; Seizure (HP:0001250): onset ; EEG with burst suppression (HP:0010851): onset ; Increased CSF glycine concentration (HP:0500230): onset ; Hyperglycinemia (HP:0002154): onset ; Respiratory failure requiring assisted ventilation (HP:0004887): onset ; Patent foramen ovale (HP:0001655): onset ; Microcephaly (HP:0000252): onset ; Hypotonia (HP:0001252): onset ; Vomiting (HP:0002013): onset ; Pyloric stenosis (HP:0002021): onset ; Micrognathia (HP:0000347): onset ; Hyperreflexia (HP:0001347): onset ; Poor suck (HP:0002033): onset ; Dysplastic corpus callosum (HP:0006989): onset ; Cerebral hypomyelination (HP:0006808): onset ; excluded: Hydrocephalus (HP:0000238): onset ; excluded: Ventriculomegaly (HP:0002119): onset
Patient 7 (MALE; P7Y5M)Glycine encephalopathy 2 (OMIM:620398)DEL:Total AMT gene deletion: chromosomal_deletion (SO:1000029)Global developmental delay (HP:0001263): onset ; Seizure (HP:0001250): onset ; EEG with burst suppression (HP:0010851): onset ; Increased CSF glycine concentration (HP:0500230): onset ; Hyperglycinemia (HP:0002154): onset ; Respiratory failure requiring assisted ventilation (HP:0004887): onset ; Microcephaly (HP:0000252): onset ; Hypotonia (HP:0001252): onset ; Micrognathia (HP:0000347): onset ; Hyperreflexia (HP:0001347): onset ; Poor suck (HP:0002033): onset ; Dysplastic corpus callosum (HP:0006989): onset ; Hydrocephalus (HP:0000238): onset ; excluded: Patent foramen ovale (HP:0001655): onset ; excluded: Vomiting (HP:0002013): onset ; excluded: Pyloric stenosis (HP:0002021): onset ; excluded: Cerebral hypomyelination (HP:0006808): onset ; excluded: Ventriculomegaly (HP:0002119): onset
" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "table = IndividualTable(cvalidator.get_error_free_individual_list())\n", + "display(HTML(table.to_html()))" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[pyphetools] Ingested 5 GA4GH phenopackets.\n", + "[INFO] Extracted 5 from 5 phenopackets with OMIM:620398\n", + "\n", + "\tGlycine encephalopathy 2 (OMIM:620398): n=5\n", + "We found a total of 21 unique HPO terms\n", + "Extracted disease: Glycine encephalopathy 2 (OMIM:620398)\n", + "Wrote HPOA disease file to OMIM-620398.tab\n" + ] + } + ], + "source": [ + "pmid = \"PMID:8005589\"\n", + "df = timporter.create_hpoa_from_phenopackets(pmid=pmid, mode_of_inheritance=Moi.AR, target=\"OMIM:620398\")" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "ps24venv", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.8" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/notebooks/AMT/input/AMT_GCE2_individuals.xlsx b/notebooks/AMT/input/AMT_GCE2_individuals.xlsx new file mode 100644 index 00000000..33a0a486 Binary files /dev/null and b/notebooks/AMT/input/AMT_GCE2_individuals.xlsx differ diff --git a/notebooks/AMT/phenopackets/PMID_33791923_Patient6.json b/notebooks/AMT/phenopackets/PMID_33791923_Patient6.json new file mode 100644 index 00000000..eb6b8d73 --- /dev/null +++ b/notebooks/AMT/phenopackets/PMID_33791923_Patient6.json @@ -0,0 +1,248 @@ +{ + "id": "PMID_33791923_Patient_6", + "subject": { + "id": "Patient 6", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P5D" + } + }, + "vitalStatus": { + "status": "DECEASED", + "timeOfDeath": { + "age": { + "iso8601duration": "P5D" + } + } + }, + "sex": "FEMALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0001263", + "label": "Global developmental delay" + } + }, + { + "type": { + "id": "HP:0001250", + "label": "Seizure" + } + }, + { + "type": { + "id": "HP:0010851", + "label": "EEG with burst suppression" + } + }, + { + "type": { + "id": "HP:0500230", + "label": "Increased CSF glycine concentration" + } + }, + { + "type": { + "id": "HP:0002154", + "label": "Hyperglycinemia" + } + }, + { + "type": { + "id": "HP:0004887", + "label": "Respiratory failure requiring assisted ventilation" + } + }, + { + "type": { + "id": "HP:0001655", + "label": "Patent foramen ovale" + } + }, + { + "type": { + "id": "HP:0000252", + "label": "Microcephaly" + } + }, + { + "type": { + "id": "HP:0001252", + "label": "Hypotonia" + } + }, + { + "type": { + "id": "HP:0002013", + "label": "Vomiting" + } + }, + { + "type": { + "id": "HP:0002021", + "label": "Pyloric stenosis" + } + }, + { + "type": { + "id": "HP:0000347", + "label": "Micrognathia" + } + }, + { + "type": { + "id": "HP:0001347", + "label": "Hyperreflexia" + } + }, + { + "type": { + "id": "HP:0002033", + "label": "Poor suck" + } + }, + { + "type": { + "id": "HP:0006989", + "label": "Dysplastic corpus callosum" + } + }, + { + "type": { + "id": "HP:0006808", + "label": "Cerebral hypomyelination" + } + }, + { + "type": { + "id": "HP:0000238", + "label": "Hydrocephalus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002119", + "label": "Ventriculomegaly" + }, + "excluded": true + } + ], + "interpretations": [ + { + "id": "Patient 6", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620398", + "label": "Glycine encephalopathy 2" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "Patient 6", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_rCaWOoHWrPHWBrADQlTqqgjNs", + "geneContext": { + "valueId": "HGNC:473", + "symbol": "AMT" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_000481.4:c.434A>T" + }, + { + "syntax": "hgvs.g", + "value": "NC_000003.12:g.49420248T>A" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr3", + "pos": "49420248", + "ref": "T", + "alt": "A" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000136", + "label": "homozygous" + } + } + } + } + ] + } + } + ], + "diseases": [ + { + "term": { + "id": "OMIM:620398", + "label": "Glycine encephalopathy 2" + }, + "onset": { + "age": { + "iso8601duration": "P2D" + } + } + } + ], + "metaData": { + "created": "2025-01-10T07:10:05.702105045Z", + "createdBy": "ORCID:0000-0002-0736-9199", + "resources": [ + { + "id": "geno", + "name": "Genotype Ontology", + "url": "http://purl.obolibrary.org/obo/geno.owl", + "version": "2022-03-05", + "namespacePrefix": "GENO", + "iriPrefix": "http://purl.obolibrary.org/obo/GENO_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "06/01/23", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "omim", + "name": "An Online Catalog of Human Genes and Genetic Disorders", + "url": "https://www.omim.org", + "version": "January 4, 2023", + "namespacePrefix": "OMIM", + "iriPrefix": "https://www.omim.org/entry/" + }, + { + "id": "so", + "name": "Sequence types and features ontology", + "url": "http://purl.obolibrary.org/obo/so.obo", + "version": "2021-11-22", + "namespacePrefix": "SO", + "iriPrefix": "http://purl.obolibrary.org/obo/SO_" + }, + { + "id": "hp", + "name": "human phenotype ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2024-12-12", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + } + ], + "phenopacketSchemaVersion": "2.0", + "externalReferences": [ + { + "id": "PMID:33791923", + "reference": "https://pubmed.ncbi.nlm.nih.gov/33791923", + "description": "Genotypic and phenotypic features in Turkish patients with classic nonketotic hyperglycinemia" + } + ] + } +} \ No newline at end of file diff --git a/notebooks/AMT/phenopackets/PMID_33791923_Patient7.json b/notebooks/AMT/phenopackets/PMID_33791923_Patient7.json new file mode 100644 index 00000000..8c3d2aaf --- /dev/null +++ b/notebooks/AMT/phenopackets/PMID_33791923_Patient7.json @@ -0,0 +1,234 @@ +{ + "id": "PMID_33791923_Patient_7", + "subject": { + "id": "Patient 7", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P7Y5M" + } + }, + "vitalStatus": { + "status": "ALIVE" + }, + "sex": "MALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0001263", + "label": "Global developmental delay" + } + }, + { + "type": { + "id": "HP:0001250", + "label": "Seizure" + } + }, + { + "type": { + "id": "HP:0010851", + "label": "EEG with burst suppression" + } + }, + { + "type": { + "id": "HP:0500230", + "label": "Increased CSF glycine concentration" + } + }, + { + "type": { + "id": "HP:0002154", + "label": "Hyperglycinemia" + } + }, + { + "type": { + "id": "HP:0004887", + "label": "Respiratory failure requiring assisted ventilation" + } + }, + { + "type": { + "id": "HP:0000252", + "label": "Microcephaly" + } + }, + { + "type": { + "id": "HP:0001252", + "label": "Hypotonia" + } + }, + { + "type": { + "id": "HP:0000347", + "label": "Micrognathia" + } + }, + { + "type": { + "id": "HP:0001347", + "label": "Hyperreflexia" + } + }, + { + "type": { + "id": "HP:0002033", + "label": "Poor suck" + } + }, + { + "type": { + "id": "HP:0006989", + "label": "Dysplastic corpus callosum" + } + }, + { + "type": { + "id": "HP:0000238", + "label": "Hydrocephalus" + } + }, + { + "type": { + "id": "HP:0001655", + "label": "Patent foramen ovale" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002013", + "label": "Vomiting" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002021", + "label": "Pyloric stenosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0006808", + "label": "Cerebral hypomyelination" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002119", + "label": "Ventriculomegaly" + }, + "excluded": true + } + ], + "interpretations": [ + { + "id": "Patient 7", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620398", + "label": "Glycine encephalopathy 2" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "Patient 7", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_AmPDvytMrhbZZpPqUGftfqTag", + "label": "DEL:Total AMT gene deletion", + "geneContext": { + "valueId": "HGNC:473", + "symbol": "AMT" + }, + "moleculeContext": "genomic", + "structuralType": { + "id": "SO:1000029", + "label": "chromosomal_deletion" + }, + "allelicState": { + "id": "GENO:0000136", + "label": "homozygous" + } + } + } + } + ] + } + } + ], + "diseases": [ + { + "term": { + "id": "OMIM:620398", + "label": "Glycine encephalopathy 2" + }, + "onset": { + "age": { + "iso8601duration": "P21D" + } + } + } + ], + "metaData": { + "created": "2025-01-10T07:10:05.702610969Z", + "createdBy": "ORCID:0000-0002-0736-9199", + "resources": [ + { + "id": "geno", + "name": "Genotype Ontology", + "url": "http://purl.obolibrary.org/obo/geno.owl", + "version": "2022-03-05", + "namespacePrefix": "GENO", + "iriPrefix": "http://purl.obolibrary.org/obo/GENO_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "06/01/23", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "omim", + "name": "An Online Catalog of Human Genes and Genetic Disorders", + "url": "https://www.omim.org", + "version": "January 4, 2023", + "namespacePrefix": "OMIM", + "iriPrefix": "https://www.omim.org/entry/" + }, + { + "id": "so", + "name": "Sequence types and features ontology", + "url": "http://purl.obolibrary.org/obo/so.obo", + "version": "2021-11-22", + "namespacePrefix": "SO", + "iriPrefix": "http://purl.obolibrary.org/obo/SO_" + }, + { + "id": "hp", + "name": "human phenotype ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2024-12-12", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + } + ], + "phenopacketSchemaVersion": "2.0", + "externalReferences": [ + { + "id": "PMID:33791923", + "reference": "https://pubmed.ncbi.nlm.nih.gov/33791923", + "description": "Genotypic and phenotypic features in Turkish patients with classic nonketotic hyperglycinemia" + } + ] + } +} \ No newline at end of file diff --git a/notebooks/AMT/phenopackets/PMID_8005589_patientA.json b/notebooks/AMT/phenopackets/PMID_8005589_patientA.json new file mode 100644 index 00000000..c6fba221 --- /dev/null +++ b/notebooks/AMT/phenopackets/PMID_8005589_patientA.json @@ -0,0 +1,146 @@ +{ + "id": "PMID_8005589_patient_A", + "subject": { + "id": "patient A", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P19Y" + } + }, + "vitalStatus": { + "status": "ALIVE" + }, + "sex": "FEMALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0001263", + "label": "Global developmental delay" + } + }, + { + "type": { + "id": "HP:0003108", + "label": "Hyperglycinuria" + } + }, + { + "type": { + "id": "HP:0010864", + "label": "Intellectual disability, severe" + } + } + ], + "interpretations": [ + { + "id": "patient A", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620398", + "label": "Glycine encephalopathy 2" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "patient A", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_qVevkShZBFtyGvImXOjAVZKbd", + "geneContext": { + "valueId": "HGNC:473", + "symbol": "AMT" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_000481.4:c.806G>A" + }, + { + "syntax": "hgvs.g", + "value": "NC_000003.12:g.49419042C>T" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr3", + "pos": "49419042", + "ref": "C", + "alt": "T" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000136", + "label": "homozygous" + } + } + } + } + ] + } + } + ], + "diseases": [ + { + "term": { + "id": "OMIM:620398", + "label": "Glycine encephalopathy 2" + } + } + ], + "metaData": { + "created": "2025-01-10T07:10:05.700823068Z", + "createdBy": "ORCID:0000-0002-0736-9199", + "resources": [ + { + "id": "geno", + "name": "Genotype Ontology", + "url": "http://purl.obolibrary.org/obo/geno.owl", + "version": "2022-03-05", + "namespacePrefix": "GENO", + "iriPrefix": "http://purl.obolibrary.org/obo/GENO_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "06/01/23", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "omim", + "name": "An Online Catalog of Human Genes and Genetic Disorders", + "url": "https://www.omim.org", + "version": "January 4, 2023", + "namespacePrefix": "OMIM", + "iriPrefix": "https://www.omim.org/entry/" + }, + { + "id": "so", + "name": "Sequence types and features ontology", + "url": "http://purl.obolibrary.org/obo/so.obo", + "version": "2021-11-22", + "namespacePrefix": "SO", + "iriPrefix": "http://purl.obolibrary.org/obo/SO_" + }, + { + "id": "hp", + "name": "human phenotype ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2024-12-12", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + } + ], + "phenopacketSchemaVersion": "2.0", + "externalReferences": [ + { + "id": "PMID:8005589", + "reference": "https://pubmed.ncbi.nlm.nih.gov/8005589", + "description": "Identification of the mutations in the T-protein gene causing typical and atypical nonketotic hyperglycinemia" + } + ] + } +} \ No newline at end of file diff --git a/notebooks/AMT/phenopackets/PMID_8005589_patientB.json b/notebooks/AMT/phenopackets/PMID_8005589_patientB.json new file mode 100644 index 00000000..91a45806 --- /dev/null +++ b/notebooks/AMT/phenopackets/PMID_8005589_patientB.json @@ -0,0 +1,193 @@ +{ + "id": "PMID_8005589_patient_B", + "subject": { + "id": "patient B", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P9Y" + } + }, + "vitalStatus": { + "status": "ALIVE" + }, + "sex": "FEMALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0001263", + "label": "Global developmental delay" + } + }, + { + "type": { + "id": "HP:0001250", + "label": "Seizure" + } + }, + { + "type": { + "id": "HP:0002059", + "label": "Cerebral atrophy" + } + }, + { + "type": { + "id": "HP:0003108", + "label": "Hyperglycinuria" + } + }, + { + "type": { + "id": "HP:0010864", + "label": "Intellectual disability, severe" + } + } + ], + "interpretations": [ + { + "id": "patient B", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620398", + "label": "Glycine encephalopathy 2" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "patient B", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_oTDoUhVcBLWgCVCgCXQsrNmmp", + "geneContext": { + "valueId": "HGNC:473", + "symbol": "AMT" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_000481.4:c.139G>A" + }, + { + "syntax": "hgvs.g", + "value": "NC_000003.12:g.49422223C>T" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr3", + "pos": "49422223", + "ref": "C", + "alt": "T" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000135", + "label": "heterozygous" + } + } + } + }, + { + "subjectOrBiosampleId": "patient B", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_rUEnxUmSjiALkuPVcPyUIAOGq", 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