Recipes
A Recipe is not a class. It is a term defined to differentiate between a specialized CategoricalVariant and a general CategoricalVariant. These recipes are pre-defined CategoricalVariants with specific constraints that represent standard categorical variants that have been identified in variant knowledgebases and registries. Implementers are encouraged to use the recipes that exist whenever possible, but are free to create new recipes as needed in a given implementation. New recipes should be shared with the community on the Cat-VRS Discussion board.
CanonicalAllele
Note
This data class is at a trial use maturity level and may change in future releases. Maturity levels are described in the GKS Maturity Model.
Computational Definition
A canonical allele is defined by an Allele that is representative of a collection of congruent Alleles, each of which depict the same nucleic acid different underlying reference sequences. Congruent representations of an Allele often exist across different genome assemblies and associated cDNA transcript representations.
Information Model
The CanonicalAllele is a Categorical Variant with exactly one constraint:
A DefiningAlleleConstraint with the .relations array containing both liftover_to and transcribed_to codes. This constraint MUST refer to a genomic variant for the allele.
Examples
The following are example implementations of that satisfy the CanonicalAllele recipe:
NM_004958.4(MTOR):c.5992_5993del (p.Met1998fs)
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0/json/example_canonicalAllele-ex1",
"title": "example_canonicalAllele-ex1",
"type": "CategoricalVariant",
"id": "clinvar:662001",
"name": "NM_004958.4(MTOR):c.5992_5993del (p.Met1998fs)",
"description": "An example canonical allele.",
"aliases": [
"NM_004958.4:c.5992_5993del",
"NC_000001.11:g.11128044_11128045del",
"NC_000001.10:g.11188101_11188102del",
"NP_004949.3:p.Met1998fs",
"NG_033239.1:g.139507_139508del",
"LRG_734:g.139507_139508del",
"LRG_734t1:c.5992_5993del"
],
"extensions": [
{
"name": "cytogenetic location",
"value": "1p36.22"
},
{
"name": "clinvar variation type",
"value": "Deletion"
},
{
"name": "hgvs list",
"value": [
{
"nucleotideExpression": {
"syntax": "hgvs.g",
"value": "NC_000001.11:g.11128044_11128045del"
},
"nucleotideType": "genomic"
},
{
"nucleotideExpression": {
"syntax": "hgvs.c",
"value": "NM_004958.4:c.5992_5993del"
},
"nucleotideType": "coding",
"maneSelect": true,
"proteinExpression": {
"syntax": "hgvs.p",
"value": "NP_004949.3:p.Met1998fs"
},
"molecularConsequence": {
"name": "frameshift_variant",
"system": "http://www.sequenceontology.org/browser/",
"systemVersion": "release_2.5.3",
"code": "SO:0001589",
"iris": [
"http://www.sequenceontology.org/browser/release_2.5.3/term/SO:0001589"
]
}
},
{
"nucleotideExpression": {
"syntax": "hgvs.g",
"value": "NG_033239.1:g.139507_139508del"
},
"nucleotideType": "genomic"
},
{
"nucleotideExpression": {
"syntax": "hgvs.g",
"value": "LRG_734:g.139507_139508del"
},
"nucleotideType": "genomic"
},
{
"nucleotideExpression": {
"syntax": "hgvs.c",
"value": "LRG_734t1:c.5992_5993del"
},
"nucleotideType": "coding"
}
]
}
],
"constraints": [
{
"type": "DefiningAlleleConstraint",
"allele": {
"id": "ga4gh:VA.0TMQdMT2OBisJ9FI4tkzaBtxGB7r8FfJ",
"type": "Allele",
"name": "NM_004958.4:c.5992_5993del",
"description": "VRS variation of NM_004958.4:c.5992_5993del, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"extensions": [
{
"name": "clinvar vcf",
"value": "1-11128043-CAT-C"
}
],
"digest": "0TMQdMT2OBisJ9FI4tkzaBtxGB7r8FfJ",
"expressions": [
{
"syntax": "spdi",
"value": "NC_000001.11:11128043:AT:"
},
{
"syntax": "hgvs.g",
"value": "NC_000001.11:g.11128044_11128045del"
},
{
"syntax": "hgvs.c",
"value": "NM_004958.4:c.5992_5993del"
},
{
"syntax": "hgvs.p",
"value": "NP_004949.1:p.Met1998fs"
}
],
"location": {
"id": "ga4gh:SL.gLe4d4Seuxn5fLCfO_2g34gF86vpGvo1",
"description": "Coding DNA (cDNA) positions 5992 to 5993 of the MTOR MANE Select coding transcript (refseq:NM_004958.4), corresponding to genomic positions 11128044 to 11128045 on chromosome 1 (refseq:NC_000001.11, GRCh38).",
"extensions": [
{
"name": "GRCh38 1-based, inclusive interval",
"value": "chr1:11128044-11128045",
"description": "Genomic positions 11128044 to 11128045 on chromosome 1 (refseq:NC_000001.11, GRCh38); 1-based, inclusive interval notation."
},
{
"name": "GRCh38 0-based, half-open interval",
"value": "chr1:11128043-11128045",
"description": "Genomic positions 11128043 to 11128045 on chromosome 1 (refseq:NC_000001.11, GRCh38); 0-based, half-open interval notation."
}
],
"type": "SequenceLocation",
"digest": "gLe4d4Seuxn5fLCfO_2g34gF86vpGvo1",
"sequenceReference": {
"id": "refseq:NM_004958.4",
"name": "NM_004958.4",
"description": "The MANE Select (GRCh38) coding transcript for MTOR.",
"aliases": [
"ensembl:ENST00000361445.9",
"ga4gh:SQ.QheGYEnKbwNpM3LulbPTBQhyBSyZwuYm"
],
"type": "SequenceReference",
"refgetAccession": "SQ.QheGYEnKbwNpM3LulbPTBQhyBSyZwuYm",
"residueAlphabet": "na"
},
"start": 6112,
"end": 6114,
"sequence": "AT"
},
"state": {
"type": "ReferenceLengthExpression",
"length": 0,
"sequence": "",
"repeatSubunitLength": 2
}
},
"relations": [
{
"primaryCoding": {
"code": "liftover_to",
"system": "ga4gh-gks-term:allele-relation"
}
},
{
"primaryCoding": {
"code": "transcribed_to",
"system": "http://www.sequenceontology.org",
"iris": [
"http://www.sequenceontology.org/browser/current_release/term/transcribed_to"
]
}
}
]
}
],
"mappings": [
{
"coding": {
"system": "https://www.ncbi.nlm.nih.gov/clinvar",
"code": "662001",
"iris": [
"https://www.ncbi.nlm.nih.gov/clinvar/variation/662001"
]
},
"relation": "exactMatch"
},
{
"coding": {
"system": "https://reg.clinicalgenome.org",
"code": "CA915941124",
"iris": [
"https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA915941124"
]
},
"relation": "relatedMatch"
},
{
"coding": {
"system": "https://varsome.com",
"code": "hg38/rs1570942058",
"iris": [
"https://varsome.com/variant/hg38/rs1570942058"
]
},
"relation": "relatedMatch"
},
{
"coding": {
"system": "https://www.ncbi.nlm.nih.gov/snp",
"code": "rs1570942058",
"iris": [
"https://www.ncbi.nlm.nih.gov/snp/rs1570942058"
]
},
"relation": "relatedMatch"
}
],
"members": [
{
"id": "ga4gh:VA.PN-6_l2_yI1UPBRCtFnWkR52iZXKVJ8b",
"type": "Allele",
"name": "NC_000001.11:g.11128044_11128045del",
"description": "VRS variation of NC_000001.11:g.11128044_11128045del, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"extensions": [
{
"name": "clinvar_vcf",
"value": "1-11128043-CAT-C"
}
],
"digest": "PN-6_l2_yI1UPBRCtFnWkR52iZXKVJ8b",
"expressions": [
{
"syntax": "spdi",
"value": "NC_000001.11:11128043:AT:"
},
{
"syntax": "hgvs.g",
"value": "NC_000001.11:g.11128044_11128045del"
},
{
"syntax": "hgvs.c",
"value": "NM_004958.4:c.5992_5993del"
},
{
"syntax": "hgvs.p",
"value": "NP_004949.1:p.Met1998fs"
}
],
"location": {
"id": "ga4gh:SL.5-SKfXZ941W7JbZW3UmQKtijyUfd6d7z",
"description": "Genomic positions 11,128,044 to 11,128,045 on chromosome 1 (refseq:NC_000001.11, GRCh38).",
"extensions": [
{
"name": "GRCh38 1-based, inclusive interval",
"value": "chr1:11128044-11128045",
"description": "Genomic positions 11,128,044 to 11,128,045 on chromosome 1 (refseq:NC_000001.11, GRCh38); 1-based, inclusive interval notation."
},
{
"name": "GRCh38 0-based, half-open interval",
"value": "chr1:11128043-11128045",
"description": "Genomic positions 11,128,043 to 11,128,045 on chromosome 1 (refseq:NC_000001.11, GRCh38); 0-based, half-open interval notation."
}
],
"type": "SequenceLocation",
"digest": "5-SKfXZ941W7JbZW3UmQKtijyUfd6d7z",
"sequenceReference": {
"id": "refseq:NC_000001.11",
"name": "NC_000001.11",
"description": "Reference sequence for GRCh38 chromosome 1.",
"aliases": [
"GRCh38:1",
"GRCh38:chr1",
"ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO"
],
"type": "SequenceReference",
"refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
"residueAlphabet": "na"
},
"start": 11128043,
"end": 11128045,
"sequence": "AT"
},
"state": {
"type": "ReferenceLengthExpression",
"length": 0,
"sequence": "",
"repeatSubunitLength": 2
}
},
{
"id": "ga4gh:VA.0TMQdMT2OBisJ9FI4tkzaBtxGB7r8FfJ",
"type": "Allele",
"name": "NM_004958.4:c.5992_5993del",
"description": "VRS variation of NM_004958.4:c.5992_5993del, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"extensions": [
{
"name": "clinvar vcf",
"value": "1-11128043-CAT-C"
}
],
"digest": "0TMQdMT2OBisJ9FI4tkzaBtxGB7r8FfJ",
"expressions": [
{
"syntax": "spdi",
"value": "NC_000001.11:11128043:AT:"
},
{
"syntax": "hgvs.g",
"value": "NC_000001.11:g.11128044_11128045del"
},
{
"syntax": "hgvs.c",
"value": "NM_004958.4:c.5992_5993del"
},
{
"syntax": "hgvs.p",
"value": "NP_004949.1:p.Met1998fs"
}
],
"location": {
"id": "ga4gh:SL.gLe4d4Seuxn5fLCfO_2g34gF86vpGvo1",
"description": "Coding DNA (cDNA) positions 5992 to 5993 of the MTOR MANE Select coding transcript (refseq:NM_004958.4), corresponding to genomic positions 11128044 to 11128045 on chromosome 1 (refseq:NC_000001.11, GRCh38).",
"extensions": [
{
"name": "GRCh38 1-based, inclusive interval",
"value": "chr1:11128044-11128045",
"description": "Genomic positions 11128044 to 11128045 on chromosome 1 (refseq:NC_000001.11, GRCh38); 1-based, inclusive interval notation."
},
{
"name": "GRCh38 0-based, half-open interval",
"value": "chr1:11128043-11128045",
"description": "Genomic positions 11128043 to 11128045 on chromosome 1 (refseq:NC_000001.11, GRCh38); 0-based, half-open interval notation."
}
],
"type": "SequenceLocation",
"digest": "gLe4d4Seuxn5fLCfO_2g34gF86vpGvo1",
"sequenceReference": {
"id": "refseq:NM_004958.4",
"name": "NM_004958.4",
"description": "The MANE Select (GRCh38) coding transcript for MTOR.",
"aliases": [
"ensembl:ENST00000361445.9",
"ga4gh:SQ.QheGYEnKbwNpM3LulbPTBQhyBSyZwuYm"
],
"type": "SequenceReference",
"refgetAccession": "SQ.QheGYEnKbwNpM3LulbPTBQhyBSyZwuYm",
"residueAlphabet": "na"
},
"start": 6112,
"end": 6114,
"sequence": "AT"
},
"state": {
"type": "ReferenceLengthExpression",
"length": 0,
"sequence": "",
"repeatSubunitLength": 2
}
}
],
"maturity": "trial use"
}
NC_000001.11:g.1699974C>G
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0/json/example_canonicalAllele-ex2",
"title": "example_canonicalAllele-ex2",
"type": "CategoricalVariant",
"id": "clingen:CA415424538",
"name": "NC_000001.11:g.1699974C>G",
"description": "An example canonical allele.",
"aliases": [
"NC_000001.11:g.1699974C>G",
"NC_000001.10:g.1631413C>G"
],
"extensions": [
{
"name": "cytogenetic location",
"value": "1p36.33"
},
{
"name": "hgvs list",
"value": [
{
"nucleotideExpression": {
"syntax": "hgvs.g",
"value": "NC_000001.11:g.1699974C>G"
}
},
{
"nucleotideExpression": {
"syntax": "hgvs.g",
"value": "NC_000001.10:g.1631413C>G"
}
}
]
}
],
"constraints": [
{
"type": "DefiningAlleleConstraint",
"allele": {
"id": "ga4gh:VA.WjRY1EXgci6Nd0M2yI86Ue_OOnfnb-Ss",
"type": "Allele",
"name": "NC_000001.11:g.1699974C>G",
"description": "VRS Allele of NC_000001.11:g.1699974C>G, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "WjRY1EXgci6Nd0M2yI86Ue_OOnfnb-Ss",
"expressions": [
{
"syntax": "hgvs.g",
"value": "NC_000001.11:g.1699974C>G"
}
],
"location": {
"id": "ga4gh:SL.YmbtK6FLqlk2bLjpFwH-y7k4RLq_t7L3",
"description": "Genomic position 1699974 on chromosome 1 (refseq:NC_000001.11, GRCh38).",
"extensions": [
{
"name": "GRCh38 1-based, genomic position",
"value": "chr1:1699974",
"description": "Genomic position 1,699,974 on chromosome 1 (refseq:NC_000001.11, GRCh38)."
},
{
"name": "GRCh38 1-based, inclusive interval notation",
"value": "chr1:1699974-1699974",
"description": "Genomic positions 1,699,974 to 1,699,974 on chromosome 1 (refseq:NC_000001.11, GRCh38); 1-based, inclusive interval notation."
},
{
"name": "GRCh38 0-based, half-open interval notation",
"value": "chr1:1699973-1699974",
"description": "Genomic positions 1,699,973 to 1,699,974 on chromosome 1 (refseq:NC_000001.11, GRCh38); 0-based, half-open interval notation."
}
],
"type": "SequenceLocation",
"digest": "YmbtK6FLqlk2bLjpFwH-y7k4RLq_t7L3",
"sequenceReference": {
"id": "refseq:NC_000001.11",
"name": "NC_000001.11",
"description": "Reference sequence for GRCh38 chromosome 1.",
"aliases": [
"GRCh38:1",
"GRCh38:chr1",
"ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO"
],
"type": "SequenceReference",
"refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
"residueAlphabet": "na"
},
"start": 1699973,
"end": 1699974,
"sequence": "C"
},
"state": {
"type": "LiteralSequenceExpression",
"sequence": "G"
}
},
"relations": [
{
"primaryCoding": {
"code": "liftover_to",
"system": "ga4gh-gks-term:allele-relation"
}
},
{
"primaryCoding": {
"code": "transcribed_to",
"system": "http://www.sequenceontology.org",
"iris": [
"http://www.sequenceontology.org/browser/current_release/term/transcribed_to"
]
}
}
]
}
],
"mappings": [
{
"coding": {
"system": "https://reg.clinicalgenome.org/",
"code": "CA415424538",
"iris": [
"https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA415424538"
]
},
"relation": "exactMatch"
},
{
"coding": {
"system": "https://www.ncbi.nlm.nih.gov/snp/",
"code": "rs1391950675",
"iris": [
"https://www.ncbi.nlm.nih.gov/snp/rs1391950675"
]
},
"relation": "relatedMatch"
},
{
"coding": {
"system": "https://gnomad.broadinstitute.org",
"code": "1-1631413-C-G",
"iris": [
"https://gnomad.broadinstitute.org/variant/1-1631413-C-G?dataset=gnomad_r2_1"
],
"extensions": [
{
"name": "dataset",
"value": "gnomad_r2_1"
}
]
},
"relation": "relatedMatch"
},
{
"coding": {
"system": "https://gnomad.broadinstitute.org",
"code": "1-1699974-C-G",
"iris": [
"https://gnomad.broadinstitute.org/variant/1-1699974-C-G?dataset=gnomad_r3"
],
"extensions": [
{
"name": "dataset",
"value": "gnomad_r3"
}
]
},
"relation": "relatedMatch"
},
{
"coding": {
"system": "https://gnomad.broadinstitute.org",
"code": "chr1-1699974-C-G",
"iris": [
"https://gnomad.broadinstitute.org/variant/chr1-1699974-C-G?dataset=gnomad_r4"
],
"extensions": [
{
"name": "dataset",
"value": "gnomad_r4"
}
]
},
"relation": "relatedMatch"
}
],
"members": [
{
"id": "ga4gh:VA.WjRY1EXgci6Nd0M2yI86Ue_OOnfnb-Ss",
"type": "Allele",
"name": "NC_000001.11:g.1699974C>G",
"description": "VRS variation of NC_000001.11:g.1699974C>G, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "WjRY1EXgci6Nd0M2yI86Ue_OOnfnb-Ss",
"expressions": [
{
"syntax": "hgvs.g",
"value": "NC_000001.11:g.1699974C>G"
}
],
"location": {
"id": "ga4gh:SL.YmbtK6FLqlk2bLjpFwH-y7k4RLq_t7L3",
"description": "Genomic position 1,699,974 on chromosome 1 (refseq:NC_000001.11, GRCh38).",
"type": "SequenceLocation",
"extensions": [
{
"name": "GRCh38 1-based, genomic position",
"value": "chr1:1699974",
"description": "Genomic position 1,699,974 on chromosome 1 (refseq:NC_000001.11, GRCh38)."
},
{
"name": "GRCh38 1-based, inclusive interval notation",
"value": "chr1:1699974-1699974",
"description": "Genomic positions 1,699,974 to 1,699,974 on chromosome 1 (refseq:NC_000001.11, GRCh38); 1-based, inclusive interval notation."
},
{
"name": "GRCh38 0-based, half-open interval notation",
"value": "chr1:1699973-1699974",
"description": "Genomic positions 1,699,973 to 1,699,974 on chromosome 1 (refseq:NC_000001.11, GRCh38); 0-based, half-open interval notation."
}
],
"digest": "YmbtK6FLqlk2bLjpFwH-y7k4RLq_t7L3",
"sequenceReference": {
"id": "refseq:NC_000001.11",
"name": "NC_000001.11",
"description": "Reference sequence for GRCh38 chromosome 1.",
"aliases": [
"GRCh38:1",
"GRCh38:chr1",
"ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO"
],
"type": "SequenceReference",
"refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
"residueAlphabet": "na"
},
"start": 1699973,
"end": 1699974,
"sequence": "C"
},
"state": {
"type": "LiteralSequenceExpression",
"sequence": "G"
}
},
{
"id": "ga4gh:VA.WW0r6Dh-z_ftn9yS-i0f1Y62JNCpVed2",
"type": "Allele",
"name": "NC_000001.10:g.1631413C>G",
"description": "VRS variation of NC_000001.10:g.1631413C>G, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "WW0r6Dh-z_ftn9yS-i0f1Y62JNCpVed2",
"expressions": [
{
"syntax": "hgvs.g",
"value": "NC_000001.10:g.1631413C>G"
}
],
"location": {
"id": "ga4gh:SL.QsC4TgLsfR6-TatBj1sVKAgfv9bGYSxb",
"description": "Genomic position 1,631,413 on chromosome 1 (refseq:NC_000001.10, GRCh37).",
"type": "SequenceLocation",
"extensions": [
{
"name": "GRCh37 1-based, genomic position",
"value": "chr1:1631413",
"description": "Genomic position 1,631,413 on chromosome 1 (refseq:NC_000001.10, GRCh37)."
},
{
"name": "GRCh37 1-based, inclusive interval notation",
"value": "chr1:1631413-1631413",
"description": "Genomic positions 1,631,413 to 1,631,413 on chromosome 1 (refseq:NC_000001.10, GRCh37); 1-based, inclusive interval notation."
},
{
"name": "GRCh37 0-based, half-open interval notation",
"value": "chr1:1631412-1631413",
"description": "Genomic positions 1,631,412 to 1,631,413 on chromosome 1 (refseq:NC_000001.10, GRCh37); 0-based, half-open interval notation."
}
],
"digest": "QsC4TgLsfR6-TatBj1sVKAgfv9bGYSxb",
"sequenceReference": {
"id": "refseq:NC_000001.10",
"name": "NC_000001.10",
"description": "Reference sequence for GRCh37 chromosome 1.",
"aliases": [
"GRCh37.1",
"GRCh37:chr1",
"ga4gh:SQ.S_KjnFVz-FE7M0W6yoaUDgYxLPc1jyWU"
],
"type": "SequenceReference",
"refgetAccession": "SQ.S_KjnFVz-FE7M0W6yoaUDgYxLPc1jyWU",
"residueAlphabet": "na"
},
"start": 1631412,
"end": 1631413,
"sequence": "C"
},
"state": {
"type": "LiteralSequenceExpression",
"sequence": "G"
}
}
],
"maturity": "trial use"
}
ProteinSequenceConsequence
Note
This data class is at a trial use maturity level and may change in future releases. Maturity levels are described in the GKS Maturity Model.
Computational Definition
A change that occurs in a protein sequence as a result of genomic changes. Due to the degenerate nature of the genetic code, there are often several genomic changes that can cause a protein sequence consequence. The protein sequence consequence, like a CanonicalAllele, is defined by an Allele that is representative of a collection of congruent Protein Alleles that share the same altered codon(s).
Information Model
The ProteinSequenceConsequence is a Categorical Variant with exactly one constraint:
A DefiningAlleleConstraint with the .relations array containing only a translation_of code. This constraint MUST refer to a protein variant for the allele.
Examples
The following are example implementations of that satisfy the ProteinSequenceConsequence recipe:
EGFR L858R
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0/json/example_proteinSequenceConsequence-ex1",
"title": "example_proteinSequenceConsequence-ex1",
"type": "CategoricalVariant",
"id": "civic.mpid:33",
"name": "EGFR L858R",
"description": "EGFR L858R has long been recognized as a functionally significant mutation in cancer, and is one of the most prevalent single mutations in lung cancer. Best described in non-small cell lung cancer (NSCLC), the mutation seems to confer sensitivity to first and second generation TKI's like gefitinib and neratinib. NSCLC patients with this mutation treated with TKI's show increased overall and progression-free survival, as compared to chemotherapy alone. Third generation TKI's are currently in clinical trials that specifically focus on mutant forms of EGFR, a few of which have shown efficacy in treating patients that failed to respond to earlier generation TKI therapies.",
"aliases": [
"LEU858ARG",
"rs121434568",
"L813R",
"LEU813ARG",
"NC_000007.13:g.55259515T>G",
"NM_005228.4:c.2573T>G",
"ENST00000275493.2:c.2573T>G",
"ENST00000275493.7:c.2573T>G",
"NP_005219.2:p.Leu858Arg"
],
"extensions": [
{
"name": "CIViC Representative Variant Coordinates",
"value": {
"chromosome": "7",
"start": 55259515,
"stop": 55259515,
"reference_bases": "T",
"variant_bases": "G",
"representative_transcript": "ENST00000275493.2",
"ensembl_version": 75,
"reference_build": "GRCh37"
}
},
{
"name": "CIViC Variant Type",
"value": {
"name": "missense_variant",
"system": "http://www.sequenceontology.org/browser/",
"systemVersion": "release_2.5.3",
"code": "SO:0001583",
"iris": [
"http://www.sequenceontology.org/browser/release_2.5.3/term/SO:0001583"
]
}
},
{
"name": "CIViC Molecular Profile Score",
"value": 379
},
{
"name": "hgvs list",
"value": [
{
"nucleotideExpression": {
"syntax": "hgvs.g",
"value": "NC_000007.13:g.55259515T>G"
},
"nucleotideType": "genomic"
},
{
"nucleotideExpression": {
"syntax": "hgvs.c",
"value": "NM_005228.5:c.2573T>G"
},
"nucleotideType": "coding"
},
{
"nucleotideExpression": {
"syntax": "hgvs.c",
"value": "ENST00000275493.2:c.2573T>G"
},
"nucleotideType": "coding"
},
{
"nucleotideExpression": {
"syntax": "hgvs.c",
"value": "ENST00000275493.7:c.2573T>G"
},
"nucleotideType": "coding",
"maneSelect": true,
"proteinExpression": {
"syntax": "hgvs.p",
"value": "NP_005219.2:p.Leu858Arg"
},
"molecularConsequence": {
"name": "missense_variant",
"system": "http://www.sequenceontology.org/browser/",
"systemVersion": "release_2.5.3",
"code": "SO:0001583",
"iris": [
"http://www.sequenceontology.org/browser/release_2.5.3/term/SO:0001583"
]
}
}
]
}
],
"constraints": [
{
"type": "DefiningAlleleConstraint",
"allele": {
"id": "ga4gh:VA.S41CcMJT2bcd8R4-qXZWH1PoHWNtG2PZ",
"type": "Allele",
"name": "NP_005219.2:p.Leu858Arg",
"description": "VRS variation of NP_005219.2:p.Leu858Arg, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "S41CcMJT2bcd8R4-qXZWH1PoHWNtG2PZ",
"expressions": [
{
"syntax": "hgvs.p",
"value": "NP_005219.2:p.Leu858Arg"
}
],
"location": {
"id": "ga4gh:SL.v0_edynH98OIu-0QPVT5anCSOriAFSDQ",
"description": "Amino acid position 858 within the EGFR protein (refseq:NP_005219.2), which is the protein product of the MANE Select (GRCh38) coding transcript for EGFR (refseq:NM_005228.5), corresponding to leucine in the reference sequence.",
"type": "SequenceLocation",
"digest": "v0_edynH98OIu-0QPVT5anCSOriAFSDQ",
"sequenceReference": {
"id": "refseq:NP_005219.2",
"name": "NP_005219.2",
"description": "The protein product of the MANE Select (GRCh38) coding transcript for EGFR (refseq:NM_005228.5), corresponding to the RefSeq protein accession NP_005219.2.",
"aliases": [
"ensembl:ENSP00000275493.2",
"ga4gh:SQ.vyo55F6mA6n2LgN4cagcdRzOuh38V4mE"
],
"type": "SequenceReference",
"refgetAccession": "SQ.vyo55F6mA6n2LgN4cagcdRzOuh38V4mE",
"residueAlphabet": "aa"
},
"start": 857,
"end": 858,
"sequence": "L"
},
"state": {
"type": "LiteralSequenceExpression",
"sequence": "R"
}
},
"relations": [
{
"primaryCoding": {
"code": "translation_of",
"system": "http://www.sequenceontology.org",
"iris": [
"http://www.sequenceontology.org/browser/current_release/term/translation_of"
]
}
}
]
}
],
"mappings": [
{
"coding": {
"system": "https://civicdb.org/variants/",
"code": "33",
"iris": [
"https://civicdb.org/variants/33/summary"
]
},
"relation": "exactMatch"
},
{
"coding": {
"system": "https://civicdb.org/molecular-profiles/",
"code": "33",
"iris": [
"https://civicdb.org/molecular-profiles/33/summary"
]
},
"relation": "relatedMatch"
},
{
"coding": {
"system": "https://reg.clinicalgenome.org/",
"code": "CA126713",
"iris": [
"https://reg.genome.network/redmine/projects/registry/genboree_registry/by_caid?caid=CA126713"
]
},
"relation": "relatedMatch"
},
{
"coding": {
"system": "https://www.ncbi.nlm.nih.gov/clinvar/variation/",
"code": "16609",
"iris": [
"https://www.ncbi.nlm.nih.gov/clinvar/variation/16609/"
]
},
"relation": "relatedMatch"
},
{
"coding": {
"system": "https://www.ncbi.nlm.nih.gov/clinvar/variation/",
"code": "376282",
"iris": [
"https://www.ncbi.nlm.nih.gov/clinvar/variation/376282/"
]
},
"relation": "relatedMatch"
},
{
"coding": {
"system": "https://www.ncbi.nlm.nih.gov/clinvar/variation/",
"code": "376280",
"iris": [
"https://www.ncbi.nlm.nih.gov/clinvar/variation/376280/"
]
},
"relation": "relatedMatch"
},
{
"coding": {
"system": "https://www.ncbi.nlm.nih.gov/snp/",
"code": "rs121434568",
"iris": [
"https://www.ncbi.nlm.nih.gov/snp/rs121434568"
]
},
"relation": "relatedMatch"
}
],
"members": [
{
"id": "ga4gh:VA.7WF8GDGgqy8ksDf9KV-qrWS_2_q8fiEO",
"type": "Allele",
"name": "NC_000007.13:g.55259515T>G",
"description": "VRS variation of NC_000007.13:g.55259515T>G, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "7WF8GDGgqy8ksDf9KV-qrWS_2_q8fiEO",
"expressions": [
{
"syntax": "hgvs.g",
"value": "NC_000007.13:g.55259515T>G"
},
{
"syntax": "hgvs.c",
"value": "NM_005228.5:c.2573T>G"
},
{
"syntax": "hgvs.p",
"value": "NP_005219.2:p.Leu858Arg"
}
],
"location": {
"id": "ga4gh:SL.FYIfdQ3NyatgqPT_kKMfeIbt00559Izo",
"description": "Genomic position 55,259,515 on chromosome 1 (refseq:NC_000007.13, GRCh38).",
"extensions": [
{
"name": "GRCh38 1-based, genomic position",
"value": "chr7:55259515",
"description": "Genomic position 55,259,515 on chromosome 1 (refseq:NC_000007.13, GRCh38)."
},
{
"name": "GRCh38 1-based, inclusive interval notation",
"value": "chr1:55259515-55259515",
"description": "Genomic positions 55,259,515 to 55,259,515 on chromosome 1 (refseq:NC_000007.13, GRCh38); 1-based, inclusive interval notation."
},
{
"name": "GRCh38 0-based, half-open interval notation",
"value": "chr1:55259514-55259515",
"description": "Genomic positions 55,259,514 to 55,259,515 on chromosome 1 (refseq:NC_000007.13, GRCh38); 0-based, half-open interval notation."
}
],
"type": "SequenceLocation",
"digest": "FYIfdQ3NyatgqPT_kKMfeIbt00559Izo",
"sequenceReference": {
"id": "refseq:NC_000007.13",
"name": "NC_000007.13",
"description": "Reference sequence for GRCh38 chromosome 7.",
"aliases": [
"GRCh38:7",
"GRCh38:chr7",
"ga4gh:SQ.IW78mgV5Cqf6M24hy52hPjyyo5tCCd86"
],
"type": "SequenceReference",
"refgetAccession": "SQ.IW78mgV5Cqf6M24hy52hPjyyo5tCCd86",
"residueAlphabet": "na"
},
"start": 55259514,
"end": 55259515,
"sequence": "AT"
},
"state": {
"type": "LiteralSequenceExpression",
"sequence": "G"
}
},
{
"id": "ga4gh:VA.gV7_dnvF8SQSeUdvgDFhU65zK_csc6VE",
"type": "Allele",
"name": "NM_005228.5:c.2573T>G",
"description": "VRS variation of NM_005228.5:c.2573T>G, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "gV7_dnvF8SQSeUdvgDFhU65zK_csc6VE",
"expressions": [
{
"syntax": "hgvs.g",
"value": "NC_000007.13:g.55259515T>G"
},
{
"syntax": "hgvs.c",
"value": "NM_005228.5:c.2573T>G"
},
{
"syntax": "hgvs.p",
"value": "NP_005219.2:p.Leu858Arg"
}
],
"location": {
"id": "ga4gh:SL.LREsUiEYvOrRhwXW1rG72kXFPegvkNzI",
"description": "Coding DNA (cDNA) position 2573 of the EGFR MANE Select coding transcript (refseq:NM_005228.5), corresponding to genomic position 55259515 on chromosome 7 (refseq:NC_000007.13, GRCh38).",
"extensions": [
{
"name": "GRCh38 1-based, genomic position",
"value": "chr7:55259515",
"description": "Genomic position 55,259,515 on chromosome 1 (refseq:NC_000007.13, GRCh38)."
},
{
"name": "GRCh38 1-based, inclusive interval notation",
"value": "chr7:55259515-55259515",
"description": "Genomic positions 55,259,515 to 55,259,515 on chromosome 1 (refseq:NC_000007.13, GRCh38); 1-based, inclusive interval notation."
},
{
"name": "GRCh38 0-based, half-open interval notation",
"value": "chr7:55259514-55259515",
"description": "Genomic positions 55,259,514 to 55,259,515 on chromosome 1 (refseq:NC_000007.13, GRCh38); 0-based, half-open interval notation."
}
],
"type": "SequenceLocation",
"digest": "LREsUiEYvOrRhwXW1rG72kXFPegvkNzI",
"sequenceReference": {
"id": "refseq:NM_005228.5",
"name": "NM_005228.5",
"description": "The MANE Select (GRCh38) coding transcript for EGFR.",
"aliases": [
"ensembl:ENST00000275493.7",
"ga4gh:SQ.d_QsP29RWJi6bac7GOC9cJ9AO7s_HUMN"
],
"type": "SequenceReference",
"refgetAccession": "SQ.d_QsP29RWJi6bac7GOC9cJ9AO7s_HUMN",
"residueAlphabet": "na"
},
"start": 2833,
"end": 2834,
"sequence": "T"
},
"state": {
"type": "LiteralSequenceExpression",
"sequence": "G"
}
},
{
"id": "ga4gh:VA.S41CcMJT2bcd8R4-qXZWH1PoHWNtG2PZ",
"type": "Allele",
"name": "NP_005219.2:p.Leu858Arg",
"description": "VRS variation of NP_005219.2:p.Leu858Arg, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "S41CcMJT2bcd8R4-qXZWH1PoHWNtG2PZ",
"expressions": [
{
"syntax": "hgvs.g",
"value": "NC_000007.13:g.55259515T>G"
},
{
"syntax": "hgvs.c",
"value": "NM_005228.5:c.2573T>G"
},
{
"syntax": "hgvs.p",
"value": "NP_005219.2:p.Leu858Arg"
}
],
"location": {
"id": "ga4gh:SL.v0_edynH98OIu-0QPVT5anCSOriAFSDQ",
"description": "Amino acid position 858 of the RefSeq protein NP_005219.2, which is the protein product of the MANE Select (GRCh38) coding transcript for EGFR (refseq:NM_005228.5).",
"type": "SequenceLocation",
"digest": "v0_edynH98OIu-0QPVT5anCSOriAFSDQ",
"sequenceReference": {
"id": "refseq:NP_005219.2",
"name": "NP_005219.2",
"description": "The protein product of the MANE Select (GRCh38) coding transcript for EGFR (refseq:NM_005228.5), corresponding to the RefSeq protein accession NP_005219.2.",
"aliases": [
"ensembl:ENSP00000275493.2",
"ga4gh:SQ.vyo55F6mA6n2LgN4cagcdRzOuh38V4mE"
],
"type": "SequenceReference",
"refgetAccession": "SQ.vyo55F6mA6n2LgN4cagcdRzOuh38V4mE",
"residueAlphabet": "aa"
},
"start": 857,
"end": 858,
"sequence": "L"
},
"state": {
"type": "LiteralSequenceExpression",
"sequence": "R"
}
}
],
"maturity": "trial use"
}
NM_007294.4(BRCA1):c.5558dup (p.Tyr1853Ter)
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0/json/example_proteinSequenceConsequence-ex2",
"title": "example_proteinSequenceConsequence-ex2",
"type": "CategoricalVariant",
"id": "clinvar:55628",
"name": "NM_007294.4(BRCA1):c.5558dup (p.Tyr1853Ter)",
"description": "An example categorical variant that models NM_007294.4(BRCA1):c.5558dup (p.Tyr1853Ter) from ClinVar.",
"aliases": [
"NM_007294.4:c.5558dup",
"NP_009225.1:p.Tyr1853Ter",
"NP_009225.1:p.Y1853*",
"NM_007294.4(BRCA1):c.5558dup (p.Y1853*)",
"NC_000017.11:g.43045712dup",
"NC_000017.10:g.41197729dup",
"NC_000017.11:43045711:T:TT"
],
"extensions": [
{
"name": "cytogenetic location",
"value": "17q21.31"
},
{
"name": "clinvar variation type",
"value": "Duplication"
},
{
"name": "hgvs list",
"value": [
{
"nucleotideExpression": {
"syntax": "hgvs.g",
"value": "NC_000017.11:g.43045712dup"
},
"nucleotideType": "genomic"
},
{
"nucleotideExpression": {
"syntax": "hgvs.g",
"value": "NC_000017.10:g.41197729dup"
},
"nucleotideType": "genomic"
},
{
"nucleotideExpression": {
"syntax": "hgvs.c",
"value": "NM_007294.4:c.5558dup"
},
"nucleotideType": "coding",
"maneSelect": true,
"proteinExpression": {
"syntax": "hgvs.p",
"value": "NP_009225.1:p.Tyr1853Ter"
},
"molecularConsequence": {
"name": "stop_gained",
"system": "http://www.sequenceontology.org/browser/",
"systemVersion": "release_2.5.3",
"code": "SO:0001587",
"iris": [
"http://www.sequenceontology.org/browser/release_2.5.3/term/SO:0001587"
]
}
}
]
}
],
"constraints": [
{
"type": "DefiningAlleleConstraint",
"allele": {
"id": "ga4gh:VA.BfZ-RbjStWkafMsFBcoSL0f4aAjHJU4n",
"type": "Allele",
"name": "NP_009225.1:p.Tyr1853Ter",
"description": "VRS variation of NP_009225.1:p.Tyr1853Ter, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "BfZ-RbjStWkafMsFBcoSL0f4aAjHJU4n",
"expressions": [
{
"syntax": "hgvs.g",
"value": "NC_000017.11:g.43045712dup"
},
{
"syntax": "hgvs.g",
"value": "NC_000017.10:g.41197729dup"
},
{
"syntax": "hgvs.c",
"value": "NM_007294.4:c.5558dup"
},
{
"syntax": "hgvs.p",
"value": "NP_009225.1:p.Tyr1853Ter"
}
],
"location": {
"id": "ga4gh:SL.bR3EOtSngkb9wNbixylsw0sNa_2HCga5",
"description": "Amino acid position 1853 of the Refseq protein NP_009225.1, which is the protein product of the MANE Select (GRCh38) coding transcript for BRCA1 (refseq:NM_007294.4).",
"type": "SequenceLocation",
"digest": "bR3EOtSngkb9wNbixylsw0sNa_2HCga5",
"sequenceReference": {
"id": "refseq:NP_009225.1",
"name": "NP_009225.1",
"description": "The protein product of the MANE Select (GRCh38) coding transcript for BRCA1 (refseq:NM_007294.4), corresponding to the Refseq protein accession NP_009225.1.",
"aliases": [
"ensembl:ENSP00000350283.3",
"ga4gh:SQ.nUzIPnHMyQV52hzgBbKl5vlbSwx8M8_Y"
],
"type": "SequenceReference",
"refgetAccession": "SQ.nUzIPnHMyQV52hzgBbKl5vlbSwx8M8_Y",
"residueAlphabet": "aa"
},
"start": 1852,
"end": 1853,
"sequence": "Y"
},
"state": {
"type": "LiteralSequenceExpression",
"sequence": "*"
}
},
"relations": [
{
"primaryCoding": {
"code": "translation_of",
"system": "http://www.sequenceontology.org",
"iris": [
"http://www.sequenceontology.org/browser/current_release/term/translation_of"
]
}
}
]
}
],
"mappings": [
{
"coding": {
"system": "https://www.ncbi.nlm.nih.gov/clinvar",
"code": "55628",
"iris": [
"https://www.ncbi.nlm.nih.gov/clinvar/variation/55628/"
]
},
"relation": "exactMatch"
},
{
"coding": {
"system": "https://reg.clinicalgenome.org/",
"code": "CA003713",
"iris": [
"https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA003713"
]
},
"relation": "relatedMatch"
},
{
"coding": {
"system": "https://www.ncbi.nlm.nih.gov/snp",
"code": "rs80357629",
"iris": [
"https://www.ncbi.nlm.nih.gov/snp/rs80357629"
]
},
"relation": "relatedMatch"
}
],
"members": [
{
"id": "ga4gh:VA.ju31SHNY7xeTI244BcOS7J78dIek46xL",
"type": "Allele",
"name": "NC_000017.11:g.43045712dup",
"description": "VRS variation of NC_000017.11:g.43045712dup, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "ju31SHNY7xeTI244BcOS7J78dIek46xL",
"expressions": [
{
"syntax": "hgvs.g",
"value": "NC_000017.11:g.43045712dup"
},
{
"syntax": "hgvs.g",
"value": "NC_000017.10:g.41197729dup"
},
{
"syntax": "hgvs.c",
"value": "NM_007294.4:c.5558dup"
},
{
"syntax": "hgvs.p",
"value": "NP_009225.1:p.Tyr1853Ter"
}
],
"location": {
"id": "ga4gh:SL.El1CbTY3p0rvxxkf5qI3YdgTo46YIjwl",
"description": "Genomic position 43,045,712 on chromosome 17 (refseq:NC_000017.11, GRCh38).",
"type": "SequenceLocation",
"extensions": [
{
"name": "GRCh38 1-based, genomic position",
"value": "chr17:43045712",
"description": "Genomic position 43,045,712 on chromosome 17 (refseq:NC_000017.11, GRCh38)."
},
{
"name": "GRCh38 1-based, inclusive interval notation",
"value": "chr17:43045712-43045712",
"description": "Genomic positions 43,045,712 to 43,045,712 on chromosome 17 (refseq:NC_000017.11, GRCh38); 1-based, inclusive interval notation."
},
{
"name": "GRCh38 0-based, half-open interval notation",
"value": "chr17:43045711-43045712",
"description": "Genomic positions 43,045,711 to 43,045,712 on chromosome 17 (refseq:NC_000017.11, GRCh38); 0-based, half-open interval notation."
}
],
"digest": "El1CbTY3p0rvxxkf5qI3YdgTo46YIjwl",
"sequenceReference": {
"id": "refseq:NC_000017.11",
"name": "NC_000017.11",
"description": "Reference sequence for GRCh38 chromosome 17",
"type": "SequenceReference",
"refgetAccession": "SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7",
"residueAlphabet": "na"
},
"start": 43045711,
"end": 43045712,
"sequence": "T"
},
"state": {
"type": "ReferenceLengthExpression",
"length": 2,
"sequence": "TT",
"repeatSubunitLength": 1
}
},
{
"id": "ga4gh:VA.UPNFCFuk1_6v7IzYbbQTV_PsYJ9WOwSa",
"type": "Allele",
"name": "NC_000017.10:g.41197729dup",
"description": "VRS variation of NC_000017.10:g.41197729dup, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "UPNFCFuk1_6v7IzYbbQTV_PsYJ9WOwSa",
"expressions": [
{
"syntax": "hgvs.g",
"value": "NC_000017.11:g.43045712dup"
},
{
"syntax": "hgvs.g",
"value": "NC_000017.10:g.41197729dup"
},
{
"syntax": "hgvs.c",
"value": "NM_007294.4:c.5558dup"
},
{
"syntax": "hgvs.p",
"value": "NP_009225.1:p.Tyr1853Ter"
}
],
"location": {
"id": "ga4gh:SL.bJxQ_soqGHGy4skIMKp6VLEB54XH32M8",
"description": "Genomic position 41,197,729 on chromosome 17 (refseq:NC_000017.10, GRCh37).",
"type": "SequenceLocation",
"extensions": [
{
"name": "GRCh37 1-based, genomic position",
"value": "chr17:41197729",
"description": "Genomic position 41,197,729 on chromosome 17 (refseq:NC_000017.10, GRCh37)."
},
{
"name": "GRCh37 1-based, inclusive interval notation",
"value": "chr17:41197729-41197729",
"description": "Genomic position 41,197,729 to 41,197,729 on chromosome 17 (refseq:NC_000017.10, GRCh37); 1-based, inclusive interval notation."
},
{
"name": "GRCh37 0-based, half-open interval notation",
"value": "chr17:41197728-41197729",
"description": "Genomic position 41,197,728 to 41,197,729 on chromosome 17 (refseq:NC_000017.10, GRCh37); 0-based, half-open interval notation."
}
],
"digest": "bJxQ_soqGHGy4skIMKp6VLEB54XH32M8",
"sequenceReference": {
"id": "refseq:NC_000017.10",
"name": "NC_000017.10",
"description": "Reference sequence for GRCh37 chromosome 17.",
"aliases": [
"GRCh37:17",
"GRCh37:chr17",
"ga4gh:SQ.AjWXsI7AkTK35XW9pgd3UbjpC3MAevlz"
],
"type": "SequenceReference",
"refgetAccession": "SQ.AjWXsI7AkTK35XW9pgd3UbjpC3MAevlz",
"residueAlphabet": "na"
},
"start": 41197728,
"end": 41197729,
"sequence": "T"
},
"state": {
"type": "ReferenceLengthExpression",
"length": 2,
"sequence": "TT",
"repeatSubunitLength": 1
}
},
{
"id": "ga4gh:VA.BfZ-RbjStWkafMsFBcoSL0f4aAjHJU4n",
"type": "Allele",
"name": "NP_009225.1:p.Tyr1853Ter",
"description": "VRS variation of NP_009225.1:p.Tyr1853Ter, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "BfZ-RbjStWkafMsFBcoSL0f4aAjHJU4n",
"expressions": [
{
"syntax": "hgvs.g",
"value": "NC_000017.11:g.43045712dup"
},
{
"syntax": "hgvs.g",
"value": "NC_000017.10:g.41197729dup"
},
{
"syntax": "hgvs.c",
"value": "NM_007294.4:c.5558dup"
},
{
"syntax": "hgvs.p",
"value": "NP_009225.1:p.Tyr1853Ter"
}
],
"location": {
"id": "ga4gh:SL.bR3EOtSngkb9wNbixylsw0sNa_2HCga5",
"description": "Amino acid position 1853 of the Refseq protein NP_009225.1, which is the protein product of the MANE Select (GRCh38) coding transcript for BRCA1 (refseq:NM_007294.4).",
"type": "SequenceLocation",
"digest": "bR3EOtSngkb9wNbixylsw0sNa_2HCga5",
"sequenceReference": {
"id": "refseq:NP_009225.1",
"name": "NP_009225.1",
"description": "The protein product of the MANE Select (GRCh38) coding transcript for BRCA1 (refseq:NM_007294.4), corresponding to the Refseq protein accession NP_009225.1.",
"aliases": [
"ensembl:ENSP00000350283.3",
"ga4gh:SQ.nUzIPnHMyQV52hzgBbKl5vlbSwx8M8_Y"
],
"type": "SequenceReference",
"refgetAccession": "SQ.nUzIPnHMyQV52hzgBbKl5vlbSwx8M8_Y",
"residueAlphabet": "aa"
},
"start": 1852,
"end": 1853,
"sequence": "Y"
},
"state": {
"type": "LiteralSequenceExpression",
"sequence": "*"
}
}
],
"maturity": "trial use"
}
CategoricalCnv
Warning
This data class is at a draft maturity level and may change significantly in future releases. Maturity levels are described in the GKS Maturity Model.
Computational Definition
A representation of the constraints for matching knowledge about CNVs.
Information Model
The CategoricalCNV is a Categorical Variant with exactly two constraints:
A DefiningLocationConstraint with the .relations array containing only a liftover_to code.
Examples
The following are example implementations of that satisfy the CategoricalCNV recipe:
GRCh38/hg38 7p22.1(chr7:5905831-6014161)x3 with CopyCountConstraint
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0/json/example_categoricalCnv-ex1",
"title": "example_categoricalCnv-ex1",
"type": "CategoricalVariant",
"id": "clinvar:151061",
"name": "GRCh38/hg38 7p22.1(chr7:5905831-6014161)x3",
"description": "An example categorical CNV that uses CopyCountConstraint.",
"aliases": [
"NC_000007.14:g.(?_5905831)_(6014161_?)dup",
"NC_000007.13:g.(?_5945462)_(6053792_?)dup"
],
"extensions": [
{
"name": "cytogenetic location",
"value": "7p22.1"
},
{
"name": "clinvar variation type",
"value": "copy number gain"
},
{
"name": "hgvs list",
"value": [
{
"nucleotideExpression": {
"syntax": "hgvs.g",
"value": "NC_000007.14:g.(?_5905831)_(6014161_?)dup"
},
"nucleotideType": "genomic"
},
{
"nucleotideExpression": {
"syntax": "hgvs.g",
"value": "NC_000007.13:g.(?_5945462)_(6053792_?)dup"
},
"nucleotideType": "genomic"
}
]
}
],
"constraints": [
{
"type": "CopyCountConstraint",
"copies": 3
},
{
"type": "DefiningLocationConstraint",
"location": {
"id": "ga4gh:SL.LChpEzYZaMug85TUqJUbT4MYgVk8vuQ7",
"description": "Genomic positions 5905831 to 6014161 on chromosome 7 (refseq:NC_000007.14, GRCh38).",
"extensions": [
{
"name": "GRCh38 1-based, inclusive interval",
"value": "chr7:5905831-6014161",
"description": "Genomic positions 5905831 to 6014161 on chromosome 7 (refseq:NC_000007.14, GRCh38); 1-based, inclusive interval notation."
},
{
"name": "GRCh38 0-based, half-open interval",
"value": "chr7:5905830-6014161",
"description": "Genomic positions 5905830 to 6014161 on chromosome 7 (refseq:NC_000007.14, GRCh38); 0-based, half-open interval notation."
}
],
"type": "SequenceLocation",
"digest": "LChpEzYZaMug85TUqJUbT4MYgVk8vuQ7",
"sequenceReference": {
"id": "refseq:NC_000007.14",
"name": "NC_000007.14",
"description": "Reference sequence for GRCh38 chromosome 7.",
"aliases": [
"GRCh38:7",
"GRCh38:chr7",
"ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul"
],
"type": "SequenceReference",
"refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul",
"residueAlphabet": "na"
},
"start": [
null,
5905830
],
"end": [
6014161,
null
]
},
"relations": [
{
"primaryCoding": {
"code": "liftover_to",
"system": "ga4gh-gks-term:allele-relation"
}
}
],
"matchCharacteristic": {
"primaryCoding": {
"code": "is_within",
"system": "ga4gh-gks-term:location-match"
}
}
}
],
"mappings": [
{
"coding": {
"system": "https://www.ncbi.nlm.nih.gov/clinvar",
"code": "151061",
"iris": [
"https://www.ncbi.nlm.nih.gov/clinvar/variation/151061"
]
},
"relation": "exactMatch"
},
{
"coding": {
"system": "https://www.ncbi.nlm.nih.gov/dbvar",
"code": "nsv930939",
"iris": [
"https://www.ncbi.nlm.nih.gov/dbvar/variants/nssv1610575/"
]
},
"relation": "relatedMatch"
}
],
"members": [
{
"id": "ga4gh:CX.W8HqtDWeVQy_pq6fOSqnPlAcNnH9vvz4",
"type": "CopyNumberCount",
"name": "NC_000007.14:g.(?_5905831)_(6014161_?)dup",
"description": "VRS variation of NC_000007.14:g.(?_5905831)_(6014161_?)dup, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "W8HqtDWeVQy_pq6fOSqnPlAcNnH9vvz4",
"expressions": [
{
"syntax": "hgvs.g",
"value": "NC_000007.14:g.(?_5905831)_(6014161_?)dup"
}
],
"location": {
"id": "ga4gh:SL.LChpEzYZaMug85TUqJUbT4MYgVk8vuQ7",
"description": "Genomic positions 5,905,831 to 6,014,161 on chromosome 7 (refseq:NC_000007.14, GRCh38).",
"extensions": [
{
"name": "GRCh38 1-based, inclusive interval",
"value": "chr7:5905831-6014161",
"description": "Genomic positions 5,905,831 to 6,014,161 on chromosome 7 (refseq:NC_000007.14, GRCh38); 1-based, inclusive interval notation."
},
{
"name": "GRCh38 0-based, half-open interval",
"value": "chr7:5905830-6014161",
"description": "Genomic positions 5,905,830 to 6,014,161 on chromosome 7 (refseq:NC_000007.14, GRCh38); 0-based, half-open interval notation."
}
],
"type": "SequenceLocation",
"digest": "LChpEzYZaMug85TUqJUbT4MYgVk8vuQ7",
"sequenceReference": {
"id": "refseq:NC_000007.14",
"name": "NC_000007.14",
"description": "Reference sequence for GRCh38 chromosome 7.",
"aliases": [
"GRCh38:7",
"GRCh38:chr7",
"ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul"
],
"type": "SequenceReference",
"refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul"
},
"start": [
null,
5905830
],
"end": [
6014161,
null
]
},
"copies": 3
},
{
"id": "ga4gh:CX.XfVcSnSqR2oJHzBMueTrgkMWg_UgbuBL",
"type": "CopyNumberCount",
"name": "NC_000007.13:g.(?_5945462)_(6053792_?)dup",
"description": "VRS variation of NC_000007.13:g.(?_5945462)_(6053792_?)dup, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "XfVcSnSqR2oJHzBMueTrgkMWg_UgbuBL",
"expressions": [
{
"syntax": "hgvs.g",
"value": "NC_000007.13:g.(?_5945462)_(6053792_?)dup"
}
],
"location": {
"id": "ga4gh:SL.9wrSvk5-4mI6CmYrt6vImSzcLssLY3VJ",
"description": "Genomic positions 5,945,462 to 6,053,792 on chromosome 7 (refseq:NC_000007.13, GRCh37).",
"extensions": [
{
"name": "GRCh37 1-based, inclusive interval",
"value": "chr7:5945462-6053792",
"description": "Genomic positions 5,945,462 to 6,053,792 on chromosome 7 (refseq:NC_000007.13, GRCh37); 1-based, inclusive interval notation."
},
{
"name": "GRCh38 0-based, half-open interval",
"value": "chr7:5945461-6053792",
"description": "Genomic positions 5,945,461 to 6,053,792 on chromosome 7 (refseq:NC_000007.13, GRCh37); 0-based, half-open interval notation."
}
],
"type": "SequenceLocation",
"digest": "9wrSvk5-4mI6CmYrt6vImSzcLssLY3VJ",
"sequenceReference": {
"id": "refseq:NC_000007.13",
"name": "NC_000007.13",
"description": "Reference sequence for GRCh37 chromosome 7.",
"aliases": [
"GRCh37:7",
"GRCh37:chr7",
"ga4gh:SQ.IW78mgV5Cqf6M24hy52hPjyyo5tCCd86"
],
"type": "SequenceReference",
"refgetAccession": "SQ.IW78mgV5Cqf6M24hy52hPjyyo5tCCd86",
"residueAlphabet": "na"
},
"start": [
null,
5945461
],
"end": [
6053792,
null
]
},
"copies": 3
}
],
"maturity": "trial use"
}
GRCh38/hg38 7p22.1(chr7:5905831-6014161)x3 with CopyChangeConstraint
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0/json/example_categoricalCnv-ex2",
"title": "example_categoricalCnv-ex2",
"type": "CategoricalVariant",
"id": "clinvar:151061",
"name": "GRCh38/hg38 7p22.1(chr7:5905831-6014161)x3",
"description": "An example categorical CNV that uses CopyChangeConstraint.",
"aliases": [
"NC_000007.14:g.(?_5905831)_(6014161_?)dup",
"NC_000007.13:g.(?_5945462)_(6053792_?)dup"
],
"extensions": [
{
"name": "cytogenetic location",
"value": "7p22.1"
},
{
"name": "clinvar variation type",
"value": "copy number gain"
},
{
"name": "hgvs list",
"value": [
{
"nucleotideExpression": {
"syntax": "hgvs.g",
"value": "NC_000007.14:g.(?_5905831)_(6014161_?)dup"
},
"nucleotideType": "genomic"
},
{
"nucleotideExpression": {
"syntax": "hgvs.g",
"value": "NC_000007.13:g.(?_5945462)_(6053792_?)dup"
},
"nucleotideType": "genomic"
}
]
}
],
"constraints": [
{
"type": "CopyChangeConstraint",
"copyChange": "gain"
},
{
"type": "DefiningLocationConstraint",
"location": {
"id": "ga4gh:SL.LChpEzYZaMug85TUqJUbT4MYgVk8vuQ7",
"name": "NC_000007.14:g.(?_5905831)_(6014161_?)",
"description": "Genomic positions 5905831 to 6014161 on chromosome 7 (refseq:NC_000007.14, GRCh38).",
"extensions": [
{
"name": "GRCh38 1-based, inclusive interval",
"value": "chr7:5905831-6014161",
"description": "Genomic positions 5905831 to 6014161 on chromosome 7 (refseq:NC_000007.14, GRCh38); 1-based, inclusive interval notation."
},
{
"name": "GRCh38 0-based, half-open interval",
"value": "chr7:5905830-6014161",
"description": "Genomic positions 5905830 to 6014161 on chromosome 7 (refseq:NC_000007.14, GRCh38); 0-based, half-open interval notation."
}
],
"type": "SequenceLocation",
"digest": "LChpEzYZaMug85TUqJUbT4MYgVk8vuQ7",
"sequenceReference": {
"id": "refseq:NC_000007.14",
"name": "NC_000007.14",
"description": "Reference sequence for GRCh38 chromosome 7.",
"aliases": [
"GRCh38:7",
"GRCh38:chr7",
"ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul"
],
"type": "SequenceReference",
"refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul",
"residueAlphabet": "na"
},
"start": [
null,
5905830
],
"end": [
6014161,
null
]
},
"relations": [
{
"primaryCoding": {
"code": "liftover_to",
"system": "ga4gh-gks-term:allele-relation"
}
}
],
"matchCharacteristic": {
"primaryCoding": {
"code": "is_within",
"system": "ga4gh-gks-term:location-match"
}
}
}
],
"mappings": [
{
"coding": {
"system": "https://www.ncbi.nlm.nih.gov/clinvar",
"code": "151061",
"iris": [
"https://www.ncbi.nlm.nih.gov/clinvar/variation/151061"
]
},
"relation": "exactMatch"
},
{
"coding": {
"system": "https://www.ncbi.nlm.nih.gov/dbvar",
"code": "nsv930939",
"iris": [
"https://www.ncbi.nlm.nih.gov/dbvar/variants/nssv1610575/"
]
},
"relation": "relatedMatch"
}
],
"members": [
{
"id": "ga4gh:CX.W8HqtDWeVQy_pq6fOSqnPlAcNnH9vvz4",
"type": "CopyNumberChange",
"name": "NC_000007.14:g.(?_5905831)_(6014161_?)dup",
"description": "VRS variation of NC_000007.14:g.(?_5905831)_(6014161_?)dup, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "W8HqtDWeVQy_pq6fOSqnPlAcNnH9vvz4",
"expressions": [
{
"syntax": "hgvs.g",
"value": "NC_000007.14:g.(?_5905831)_(6014161_?)dup"
}
],
"location": {
"id": "ga4gh:SL.LChpEzYZaMug85TUqJUbT4MYgVk8vuQ7",
"description": "Genomic positions 5905831 to 6014161 on chromosome 7 (refseq:NC_000007.14, GRCh38).",
"extensions": [
{
"name": "GRCh38 1-based, inclusive interval",
"value": "chr7:5905831-6014161",
"description": "Genomic positions 5905831 to 6014161 on chromosome 7 (refseq:NC_000007.14, GRCh38); 1-based, inclusive interval notation."
},
{
"name": "GRCh38 0-based, half-open interval",
"value": "chr7:5905830-6014161",
"description": "Genomic positions 5905830 to 6014161 on chromosome 7 (refseq:NC_000007.14, GRCh38); 0-based, half-open interval notation."
}
],
"type": "SequenceLocation",
"digest": "LChpEzYZaMug85TUqJUbT4MYgVk8vuQ7",
"sequenceReference": {
"id": "refseq:NC_000007.14",
"name": "NC_000007.14",
"description": "Reference sequence for GRCh38 chromosome 7.",
"aliases": [
"GRCh38:7",
"GRCh38:chr7",
"ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul"
],
"type": "SequenceReference",
"refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul"
},
"start": [
null,
5905830
],
"end": [
6014161,
null
]
},
"copyChange": "gain"
},
{
"id": "ga4gh:CX.XfVcSnSqR2oJHzBMueTrgkMWg_UgbuBL",
"type": "CopyNumberChange",
"name": "NC_000007.13:g.(?_5945462)_(6053792_?)dup",
"description": "VRS variation of NC_000007.13:g.(?_5945462)_(6053792_?)dup, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "XfVcSnSqR2oJHzBMueTrgkMWg_UgbuBL",
"expressions": [
{
"syntax": "hgvs.g",
"value": "NC_000007.13:g.(?_5945462)_(6053792_?)dup"
}
],
"location": {
"id": "ga4gh:SL.9wrSvk5-4mI6CmYrt6vImSzcLssLY3VJ",
"description": "Genomic positions 5945462 to 6053792 on chromosome 7 (refseq:NC_000007.13, GRCh37).",
"extensions": [
{
"name": "GRCh37 1-based, inclusive interval",
"value": "chr7:5945462-6053792",
"description": "Genomic positions 5945462 to 6053792 on chromosome 7 (refseq:NC_000007.13, GRCh37); 1-based, inclusive interval notation."
},
{
"name": "GRCh38 0-based, half-open interval",
"value": "chr7:5945461-6053792",
"description": "Genomic positions 5945461 to 6053792 on chromosome 7 (refseq:NC_000007.13, GRCh37); 0-based, half-open interval notation."
}
],
"type": "SequenceLocation",
"digest": "9wrSvk5-4mI6CmYrt6vImSzcLssLY3VJ",
"sequenceReference": {
"id": "refseq:NC_000007.13",
"name": "NC_000007.13",
"description": "Reference sequence for GRCh37 chromosome 7.",
"aliases": [
"GRCh37:7",
"GRCh37:chr7",
"ga4gh:SQ.IW78mgV5Cqf6M24hy52hPjyyo5tCCd86"
],
"type": "SequenceReference",
"refgetAccession": "SQ.IW78mgV5Cqf6M24hy52hPjyyo5tCCd86",
"residueAlphabet": "na"
},
"start": [
null,
5945461
],
"end": [
6053792,
null
]
},
"copyChange": "gain"
}
],
"maturity": "trial use"
}
GRCh38 Xp22.31(chrX:6978350-7594949)x3
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0/json/example_categoricalCnv-ex3",
"title": "example_categoricalCnv-ex3",
"type": "CategoricalVariant",
"id": "clingen:cacn42032202",
"name": "GRCh38 Xp22.31(chrX:6978350-7594949)x3",
"description": "An example categoricalCNV that uses CopyCountConstraint and uses ranges for start/end positions within the DefiningLocationConstraint.",
"aliases": [
"NC_000023.11:g.(6978350_6996235)_(7564455_7594949)dup(2)",
"GRCh37 (chrX:6896391_6914276-7482496_7512990)x3",
"NC_000023.10:g.(6896391_6914276-7482496_7512990)dup(2)"
],
"extensions": [
{
"name": "cytogenetic location",
"value": "Xp22.31"
}
],
"constraints": [
{
"type": "CopyCountConstraint",
"copies": 3
},
{
"type": "DefiningLocationConstraint",
"location": {
"id": "ga4gh:SL.XyercAFM_APQwFaDuPcXG5lHa4wUpkiL",
"description": "Genomic region between positions 6,978,350-7,594,949 on chromosome X (refseq:NC_000023.11, GRCh38), with breakpoints estimated within the intervals 6,978,350-6,996,235 and 7,564,455-7,594,949.",
"extensions": [
{
"name": "GRCh38 1-based, inclusive interval",
"value": "chrX:(6978350\u20136996235)-(7564455\u20137594949)",
"description": "Genomic region between positions 6,978,350-7,594,949 on chromosome X (refseq:NC_000023.11, GRCh38), with breakpoints estimated within the intervals 6,978,350-6,996,235 and 7,564,455-7,594,949; 1-based, inclusive interval notation."
},
{
"name": "GRCh38 0-based, half-open interval",
"value": "chrX:(6978349\u20136996235)-(7564454\u20137594949)",
"description": "Genomic region between positions 6,978,349-7,594,949 on chromosome X (refseq:NC_000023.11, GRCh38), with breakpoints estimated within the intervals 6,978,349-6,996,235 and 7,564,454-7,594,949; 0-based, half-open interval notation."
}
],
"type": "SequenceLocation",
"digest": "XyercAFM_APQwFaDuPcXG5lHa4wUpkiL",
"sequenceReference": {
"id": "refseq:NC_000023.11",
"name": "NC_000023.11",
"description": "Reference sequence for GRCh38 chromosome X.",
"aliases": [
"GRCh38:X",
"GRCh38:chrX",
"ga4gh:SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP"
],
"type": "SequenceReference",
"refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul"
},
"start": [
6978350,
6996235
],
"end": [
7564455,
7594949
]
},
"relations": [
{
"primaryCoding": {
"code": "liftover_to",
"system": "ga4gh-gks-term:allele-relation"
}
}
],
"matchCharacteristic": {
"primaryCoding": {
"code": "is_within",
"system": "ga4gh-gks-term:location-match"
}
}
}
],
"mappings": [
{
"coding": {
"system": "https://reg.clinicalgenome.org/",
"code": "CACN42032202",
"iris": [
"https://reg.clinicalgenome.org/redmine/projects/Registry/genboree_registry/by_canonicalid?canonicalid=CACN42032202"
]
},
"relation": "exactMatch"
}
],
"members": [
{
"id": "ga4gh:CX.Xb6kSRqlCY2VS1QJeKxhWyGqPfpPigf3",
"type": "CopyNumberCount",
"name": "NC_000023.11:g.(6978350_6996235)_(7564455_7594949)dup(2)",
"description": "VRS variation of NC_000023.11:g.(6978350_6996235)_(7564455_7594949)dup, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "Xb6kSRqlCY2VS1QJeKxhWyGqPfpPigf3",
"expressions": [
{
"syntax": "hgvs.g",
"value": "NC_000023.11:g.(6978350_6996235)_(7564455_7594949)dup"
}
],
"location": {
"id": "ga4gh:SL.XyercAFM_APQwFaDuPcXG5lHa4wUpkiL",
"description": "Genomic region between positions 6,978,350-7,594,949 on chromosome X (refseq:NC_000023.11, GRCh38), with breakpoints estimated within the intervals 6,978,350-6,996,235 and 7,564,455-7,594,949.",
"extensions": [
{
"name": "GRCh38 1-based, inclusive interval",
"value": "chrX:(6978350\u20136996235)-(7564455\u20137594949)",
"description": "Genomic region between positions 6,978,350-7,594,949 on chromosome X (refseq:NC_000023.11, GRCh38), with breakpoints estimated within the intervals 6,978,350-6,996,235 and 7,564,455-7,594,949; 1-based, inclusive interval notation."
},
{
"name": "GRCh38 0-based, half-open interval",
"value": "chrX:(6978349\u20136996235)-(7564454\u20137594949)",
"description": "Genomic region between positions 6,978,349-7,594,949 on chromosome X (refseq:NC_000023.11, GRCh38), with breakpoints estimated within the intervals 6,978,349-6,996,235 and 7,564,454-7,594,949; 0-based, half-open interval notation."
}
],
"type": "SequenceLocation",
"digest": "XyercAFM_APQwFaDuPcXG5lHa4wUpkiL",
"sequenceReference": {
"id": "refseq:NC_000023.11",
"name": "NC_000023.11",
"description": "Reference sequence for GRCh38 chromosome X.",
"aliases": [
"GRCh38:X",
"GRCh38:chrX",
"ga4gh:SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP"
],
"type": "SequenceReference",
"refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul"
},
"start": [
6978350,
6996235
],
"end": [
7564455,
7594949
]
},
"copies": 3
}
],
"maturity": "trial use"
}
TP53 Loss
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0/json/example_categoricalCnv-ex4",
"title": "example_categoricalCnv-ex4",
"type": "CategoricalVariant",
"id": "civic.vid:4452",
"name": "TP53 Loss",
"description": "TP53 Copy Number Loss is a categorical copy-number variant resulting from the deletion of one copy of the TP53 gene.",
"aliases": [
"TP53 Copy Number Loss"
],
"extensions": [
{
"name": "cytogenetic location",
"value": "17p13"
}
],
"constraints": [
{
"type": "FeatureContextConstraint",
"featureContext": {
"id": "TP53",
"name": "TP53",
"conceptType": "gene",
"primaryCoding": [
{
"id": "hgnc:11998",
"name": "TP53",
"system": "https://genenames.org",
"code": "HGNC:11998",
"iris": [
"https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:11998"
]
}
],
"extensions": [
{
"name": "cytogenetic location",
"value": "17p13.1"
}
]
}
},
{
"type": "CopyChangeConstraint",
"copyChange": "loss"
}
],
"members": [],
"mappings": [
{
"coding": {
"name": "TP53 Loss",
"system": "https://civicdb.org",
"code": "civic.vid:4452",
"iris": [
"https://civicdb.org/variants/4452/summary"
]
},
"relation": "exactMatch"
},
{
"coding": {
"name": "TP53 Deletion",
"system": "https://civicdb.org/",
"code": "civic.mpid:4456",
"iris": [
"https://civicdb.org/molecular-profiles/4456/summary"
]
},
"relation": "relatedMatch"
}
],
"maturity": "trial use"
}