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functionVariant-ex3.json
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156 lines (156 loc) · 5.87 KB
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{
"id": "civic.mpid:1150",
"type": "CategoricalVariant",
"name": "PIK3CA p.R38H",
"description": "An example categorical variant that uses DefiningAlleleConstraint, FeatureContextConstraint, and FunctionConstraint.",
"constraints": [
{
"type": "DefiningAlleleConstraint",
"allele": {
"id": "ga4gh:VA.gFYUMkeAme8HeNqcBIDPYIB45_xRa9Qi",
"type": "Allele",
"name": "NM_006218.4:c.113G>A",
"description": "VRS Variation of NM_006218.4:c.113G>A, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "gFYUMkeAme8HeNqcBIDPYIB45_xRa9Qi",
"expressions": [
{
"syntax": "hgvs.c",
"value": "NM_006218.4:c.113G>A"
}
],
"location": {
"id": "ga4gh:SL.rZhFJCEGRkU-G3EqaGuUpefj2bP94NLi",
"description": "Coding DNA (cDNA) position 113 of the PIK3CA MANE Select coding transcript (refseq:NM_006218.4), corresponding to genomic position 179198938 on chromosome 3 (refseq:NC_000003.12, GRCh38).",
"extensions": [
{
"name": "GRCh38, 1-based, genomic position",
"value": "chr3:179198938",
"description": "Genomic position 179,198,938 on chromosome 3 (refseq:NC_000003.12, GRCh38)."
},
{
"name": "GRCh38, 1-based, inclusive interval notation",
"value": "chr3:179198938-179198938",
"description": "Genomic positions 179,198,938 to 179,198,938 on chromosome 3 (refseq:NC_000003.12, GRCh38)."
},
{
"name": "GRCh38, 0-based, half-open interval notation",
"value": "chr3:179198937-179198938",
"description": "Genomic positions 179,198,937 to 179,198,938 on chromosome 3 (refseq:NC_000003.12, GRCh38)."
}
],
"type": "SequenceLocation",
"digest": "rZhFJCEGRkU-G3EqaGuUpefj2bP94NLi",
"sequenceReference": {
"id": "refseq:NM_006218.4",
"name": "NM_006218.4",
"description": "The MANE Select (GRCh38) coding transcript for PIK3CA.",
"aliases": [
"ensembl:ENST00000263967.4",
"ga4gh:SQ.vV37R3hERpo6hA6RBsi9AaaMoY7ELvk9"
],
"type": "SequenceReference",
"refgetAccession": "SQ.vV37R3hERpo6hA6RBsi9AaaMoY7ELvk9",
"residueAlphabet": "na"
},
"start": 435,
"end": 436,
"sequence": "G"
},
"state": {
"type": "LiteralSequenceExpression",
"sequence": "A"
}
}
},
{
"type": "FeatureContextConstraint",
"featureContext": {
"id": "hgnc:8975",
"conceptType": "Gene",
"name": "PIK3CA",
"primaryCoding": {
"id": "hgnc:8975",
"system": "https://www.genenames.org",
"code": "HGNC:8975",
"iris": [
"https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:8975"
]
}
}
},
{
"type": "FunctionConstraint",
"functionConsequence": {
"id": "SO:0002053",
"name": "gain of function",
"primaryCoding": {
"id": "SO:0002053",
"name": "gain_of_function",
"system": "http://www.sequenceontology.org",
"code": "SO:0002053",
"iris": [
"http://www.sequenceontology.org/browser/current_release/term/SO:0002053"
]
}
},
"description": "Function consequence described as gain of function using Sequence Ontology."
}
],
"members": [
{
"id": "ga4gh:VA.gFYUMkeAme8HeNqcBIDPYIB45_xRa9Qi",
"type": "Allele",
"name": "NM_006218.4:c.113G>A",
"description": "VRS Variation of NM_006218.4:c.113G>A, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "gFYUMkeAme8HeNqcBIDPYIB45_xRa9Qi",
"expressions": [
{
"syntax": "hgvs.c",
"value": "NM_006218.4:c.113G>A"
}
],
"location": {
"id": "ga4gh:SL.rZhFJCEGRkU-G3EqaGuUpefj2bP94NLi",
"description": "Coding DNA (cDNA) position 113 of the PIK3CA MANE Select coding transcript (refseq:NM_006218.4), corresponding to genomic position 179198938 on chromosome 3 (refseq:NC_000003.12, GRCh38).",
"extensions": [
{
"name": "GRCh38, 1-based, genomic position",
"value": "chr3:179198938",
"description": "Genomic position 179,198,938 on chromosome 3 (refseq:NC_000003.12, GRCh38)."
},
{
"name": "GRCh38, 1-based, inclusive interval notation",
"value": "chr3:179198938-179198938",
"description": "Genomic positions 179,198,938 to 179,198,938 on chromosome 3 (refseq:NC_000003.12, GRCh38)."
},
{
"name": "GRCh38, 0-based, half-open interval notation",
"value": "chr3:179198937-179198938",
"description": "Genomic positions 179,198,937 to 179,198,938 on chromosome 3 (refseq:NC_000003.12, GRCh38)."
}
],
"type": "SequenceLocation",
"digest": "rZhFJCEGRkU-G3EqaGuUpefj2bP94NLi",
"sequenceReference": {
"id": "refseq:NM_006218.4",
"name": "NM_006218.4",
"description": "The MANE Select (GRCh38) coding transcript for PIK3CA.",
"aliases": [
"ensembl:ENST00000263967.4",
"ga4gh:SQ.vV37R3hERpo6hA6RBsi9AaaMoY7ELvk9"
],
"type": "SequenceReference",
"refgetAccession": "SQ.vV37R3hERpo6hA6RBsi9AaaMoY7ELvk9",
"residueAlphabet": "na"
},
"start": 435,
"end": 436,
"sequence": "G"
},
"state": {
"type": "LiteralSequenceExpression",
"sequence": "A"
}
}
]
}