BRAF V600
Source: CIViC variant id 17: BRAF V600 (annotated)
Recipes that this example satisfies: None
This is the annotated version of BRAF V600. It is structurally equivalent to that example and includes inline YAML comments throughout the source file explaining the role and rationale of each field. This version is intended for readers learning to work with the Cat-VRS specification.
Attributes
id: civic.vid:17, where vid stands for Variant ID, derived from the Variant ID contained within the CIViC URL for this genomic alteration.type: CategoricalVariant, as required by the specification.name: BRAF V600, the human-readable name for this variant.description: A summary of the categorical variant noting that BRAF V600 variants are missense amino acid substitutions that result in a change at valine 600, with V600E being the most common and V600K, V600M, V600R, and V600G also observed.aliases: Representations with the MANE Select transcript for BRAF: NM_004333.6(BRAF) V600 and NM_004333.6 V600.extensions: The CIViC Representative Variant Coordinates are included, specifying GRCh37 genomic coordinates on chromosome 7.mappings: A set of ClinVar variants corresponding to amino acid substitutions at BRAF V600 are included as relatedMatch mappings: V600E (c.1799T>A), V600R (c.1798_1799delinsAG), V600K (c.1798_1799delinsAA), V600G (c.1799T>G), and V600M (c.1798G>A).
Constraints
Defining Location Constraint: The defining location is amino acid position 600 within the BRAF protein (refseq:NP_004324.2), the protein product of the MANE Select coding transcript for BRAF (refseq:NM_004333.6), corresponding to valine in the reference sequence. The matchCharacteristic is set to is_within, meaning any variant whose affected residue falls within this position satisfies the constraint.
Members
The members field includes five VRS Allele objects generated using the VICC Variation Normalizer from the hgvs.c representations of BRAF V600E (NM_004333.6:c.1799T>A), V600K (NM_004333.6:c.1798_1799delinsAA), V600G (NM_004333.6:c.1799T>G), V600M (NM_004333.6:c.1798G>A), and V600R (NM_004333.6:c.1798_1799delinsAG).
Full example: JSON
{
"id": "civic.vid:17",
"type": "CategoricalVariant",
"name": "BRAF V600",
"description": "BRAF V600 variants are missense amino acid substitutions that result in Valine changed. V600E is the most common substitution, but V600K, V600M, V600R, and V600G have also been observed.",
"aliases": [
"NM_004333.6(BRAF) V600",
"NM_004333.6 V600"
],
"extensions": [
{
"name": "CIViC Representative Variant Coordinates",
"value": {
"chromosome": "7",
"start": 140453136,
"stop": 140453137,
"reference_bases": "",
"variant_bases": "",
"representative_transcript": "ENST00000288602.6",
"ensembl_version": 75,
"reference_build": "GRCh37"
}
}
],
"constraints": [
{
"type": "DefiningLocationConstraint",
"location": {
"id": "ga4gh:SL.1ReS370wzmC9PGTn13XrnG8Ot7UAKYuw",
"description": "Amino acid position 600 within the BRAF protein (refseq:NP_004324.2), which is the protein product of the MANE Select (GRCh38) coding transcript for BRAF (refseq:NM_004333.6), corresponding to valine in the reference sequence.",
"type": "SequenceLocation",
"digest": "1ReS370wzmC9PGTn13XrnG8Ot7UAKYuw",
"sequenceReference": {
"id": "refseq:NP_004324.2",
"name": "NP_004324.2",
"description": "The protein product of the MANE Select (GRCh38) coding transcript for BRAF (refseq:NM_004333.6), corresponding to the Refseq protein accession NP_004324.2.",
"aliases": [
"ensembl:ENSP00000288602.6",
"ga4gh:SQ.cQvw4UsHHRRlogxbWCB8W-mKD4AraM9y"
],
"type": "SequenceReference",
"refgetAccession": "SQ.cQvw4UsHHRRlogxbWCB8W-mKD4AraM9y",
"residueAlphabet": "aa"
},
"start": 599,
"end": 600,
"sequence": "V"
},
"relations": [
{
"primaryCoding": {
"code": "translation_of",
"system": "http://www.sequenceontology.org",
"iris": [
"http://www.sequenceontology.org/browser/current_release/term/translation_of"
]
}
}
],
"matchCharacteristic": {
"primaryCoding": {
"code": "is_within",
"system": "ga4gh-gks-term:location-match"
}
}
}
],
"mappings": [
{
"coding": {
"system": "https://www.ncbi.nlm.nih.gov/clinvar/variation/",
"code": "13961",
"name": "NM_004333.6(BRAF):c.1799T>A (p.Val600Glu)",
"iris": [
"https://www.ncbi.nlm.nih.gov/clinvar/variation/13961"
]
},
"relation": "relatedMatch"
},
{
"coding": {
"system": "https://www.ncbi.nlm.nih.gov/clinvar/variation/",
"code": "375940",
"name": "NM_004333.6(BRAF):c.1798_1799delinsAG (p.Val600Arg)",
"iris": [
"https://www.ncbi.nlm.nih.gov/clinvar/variation/375940"
]
},
"relation": "relatedMatch"
},
{
"coding": {
"system": "https://www.ncbi.nlm.nih.gov/clinvar/variation/",
"code": "375941",
"name": "NM_004333.6(BRAF):c.1798_1799delinsAA (p.Val600Lys)",
"iris": [
"https://www.ncbi.nlm.nih.gov/clinvar/variation/375941"
]
},
"relation": "relatedMatch"
},
{
"coding": {
"system": "https://www.ncbi.nlm.nih.gov/clinvar/variation/",
"code": "40389",
"name": "NM_004333.6(BRAF):c.1799T>G (p.Val600Gly)",
"iris": [
"https://www.ncbi.nlm.nih.gov/clinvar/variation/40389"
]
},
"relation": "relatedMatch"
},
{
"coding": {
"system": "https://www.ncbi.nlm.nih.gov/clinvar/variation/",
"code": "44815",
"name": "NM_004333.6(BRAF):c.1798G>A (p.Val600Met)",
"iris": [
"https://www.ncbi.nlm.nih.gov/clinvar/variation/44815"
]
},
"relation": "relatedMatch"
}
],
"members": [
{
"id": "ga4gh:VA.W6xsV-aFm9yT2Bic5cFAV2j0rll6KK5R",
"type": "Allele",
"name": "NM_004333.6:c.1799T>A",
"description": "VRS variation of NM_004333.6:c.1799T>A, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "W6xsV-aFm9yT2Bic5cFAV2j0rll6KK5R",
"expressions": [
{
"syntax": "hgvs.c",
"value": "NM_004333.6:c.1799T>A"
}
],
"location": {
"id": "ga4gh:SL.8HBKs9fzlT3tKWlM03REjkg_0Om6Y33U",
"description": "Coding DNA (cDNA) position 1799 of the BRAF MANE Select coding transcript (refseq:NM_004333.6), corresponding to genomic position 140753336 on chromosome 7 (refseq:NC_000007.14, GRCh38).",
"extensions": [
{
"name": "GRCh38 1-based, genomic position",
"value": "chr7:140753336",
"description": "Genomic position 140,753,336 on chromosome 7 (refseq:NC_000007.14, GRCh38)."
},
{
"name": "GRCh38 1-based, inclusive interval",
"value": "chr7:140753336-140753336",
"description": "Genomic positions 140,753,336 to 140,753,336 on chromosome 7 (refseq:NC_000007.14, GRCh38); 1-based, inclusive interval notation."
},
{
"name": "GRCh38 0-based, half-open interval",
"value": "chr7:140753335-140753337",
"description": "Genomic positions 140,753,335 to 140,753,336 on chromosome 7 (refseq:NC_000007.14, GRCh38); 0-based, half-open interval notation."
}
],
"type": "SequenceLocation",
"digest": "8HBKs9fzlT3tKWlM03REjkg_0Om6Y33U",
"sequenceReference": {
"id": "refseq:NM_004333.6",
"name": "NM_004333.6",
"description": "The MANE Select (GRCh38) coding transcript for BRAF.",
"aliases": [
"ga4gh:SQ.aKMPEJgmlZXt_F6gRY5cUG3THH2n-GUa"
],
"type": "SequenceReference",
"refgetAccession": "SQ.aKMPEJgmlZXt_F6gRY5cUG3THH2n-GUa",
"residueAlphabet": "na"
},
"start": 2024,
"end": 2025,
"sequence": "T"
},
"state": {
"type": "LiteralSequenceExpression",
"sequence": "A"
}
},
{
"id": "ga4gh:VA.GIOeMJX8rJ-q9ZGqmFRIUOGnXQ5NARht",
"type": "Allele",
"name": "NM_004333.6:c.1798_1799delinsAA",
"description": "VRS variation of NM_004333.6:c.1798_1799delinsAA, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "GIOeMJX8rJ-q9ZGqmFRIUOGnXQ5NARht",
"expressions": [
{
"syntax": "hgvs.c",
"value": "NM_004333.6:c.1798_1799delinsAA"
}
],
"location": {
"id": "ga4gh:SL.SXY8ShFrBAfSvtO_sXLMQKN3Ozc5awgh",
"description": "Coding DNA (cDNA) positions 1798 to 1799 of the BRAF MANE Select coding transcript (refseq:NM_004333.6), corresponding to genomic positions 140753336 to 140753337 on chromosome 7 (refseq:NC_000007.14, GRCh38).",
"extensions": [
{
"name": "GRCh38 1-based, inclusive interval",
"value": "chr7:140753336-140753337",
"description": "Genomic positions 140,753,336 to 140,753,337 on chromosome 7 (refseq:NC_000007.14, GRCh38); 1-based, inclusive interval notation."
},
{
"name": "GRCh38 0-based, half-open interval",
"value": "chr7:140753335-140753337",
"description": "Genomic positions 140,753,335 to 140,753,337 on chromosome 7 (refseq:NC_000007.14, GRCh38); 0-based, half-open interval notation."
}
],
"type": "SequenceLocation",
"digest": "SXY8ShFrBAfSvtO_sXLMQKN3Ozc5awgh",
"sequenceReference": {
"id": "refseq:NM_004333.6",
"name": "NM_004333.6",
"description": "The MANE Select (GRCh38) coding transcript for BRAF.",
"aliases": [
"ga4gh:SQ.aKMPEJgmlZXt_F6gRY5cUG3THH2n-GUa"
],
"type": "SequenceReference",
"refgetAccession": "SQ.aKMPEJgmlZXt_F6gRY5cUG3THH2n-GUa",
"residueAlphabet": "na"
},
"start": 2023,
"end": 2025,
"sequence": "GT"
},
"state": {
"type": "LiteralSequenceExpression",
"sequence": "AA"
}
},
{
"id": "ga4gh:VA.PEphL_4Hx5JYuJPMzgu0pRQIUcz_J9p0",
"type": "Allele",
"name": "NM_004333.6:c.1799T>G",
"description": "VRS variation of NM_004333.6:c.1799T>G, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "PEphL_4Hx5JYuJPMzgu0pRQIUcz_J9p0",
"expressions": [
{
"syntax": "hgvs.c",
"value": "NM_004333.6:c.1799T>G"
}
],
"location": {
"id": "ga4gh:SL.8HBKs9fzlT3tKWlM03REjkg_0Om6Y33U",
"description": "Coding DNA (cDNA) positions 1799 of the BRAF MANE Select coding transcript (refseq:NM_004333.6), corresponding to genomic position 140753336 on chromosome 7 (refseq:NC_000007.14, GRCh38).",
"extensions": [
{
"name": "GRCh38 1-based, genomic position",
"value": "chr7:140753336",
"description": "Genomic position 140,753,336 on chromosome 7 (refseq:NC_000007.14, GRCh38)."
},
{
"name": "GRCh38 1-based, inclusive interval",
"value": "chr7:140753336-140753336",
"description": "Genomic positions 140,753,336 to 140,753,336 on chromosome 7 (refseq:NC_000007.14, GRCh38); 1-based, inclusive interval notation."
},
{
"name": "GRCh38 0-based, half-open interval",
"value": "chr7:140753335-140753336",
"description": "Genomic positions 140,753,335 to 140,753,336 on chromosome 7 (refseq:NC_000007.14, GRCh38); 0-based, half-open interval notation."
}
],
"type": "SequenceLocation",
"digest": "8HBKs9fzlT3tKWlM03REjkg_0Om6Y33U",
"sequenceReference": {
"id": "refseq:NM_004333.6",
"name": "NM_004333.6",
"description": "The MANE Select (GRCh38) coding transcript for BRAF.",
"aliases": [
"ga4gh:SQ.aKMPEJgmlZXt_F6gRY5cUG3THH2n-GUa"
],
"type": "SequenceReference",
"refgetAccession": "SQ.aKMPEJgmlZXt_F6gRY5cUG3THH2n-GUa",
"residueAlphabet": "na"
},
"start": 2024,
"end": 2025,
"sequence": "T"
},
"state": {
"type": "LiteralSequenceExpression",
"sequence": "G"
}
},
{
"id": "ga4gh:VA.O3Wd-kD48Dl1ihRUuf4vVybLaXYKFXnk",
"name": "NM_004333.6:c.1798G>A",
"description": "VRS variation of NM_004333.6:c.1799T>A, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "O3Wd-kD48Dl1ihRUuf4vVybLaXYKFXnk",
"expressions": [
{
"syntax": "hgvs.c",
"value": "NM_004333.6:c.1798G>A"
}
],
"type": "Allele",
"location": {
"id": "ga4gh:SL.1ReS370wzmC9PGTn13XrnG8Ot7UAKYuw",
"description": "Coding DNA (cDNA) position 1798 of the BRAF MANE Select coding transcript (refseq:NM_004333.6), corresponding to genomic position 140753337 on chromosome 7 (refseq:NC_000007.14, GRCh38).",
"extensions": [
{
"name": "GRCh38 1-based, genomic position",
"value": "chr7:140753337",
"description": "Genomic position 140,753,337 on chromosome 7 (refseq:NC_000007.14, GRCh38)."
},
{
"name": "GRCh38 1-based, inclusive interval",
"value": "chr7:140753337-140753337",
"description": "Genomic positions 140,753,337 to 140,753,337 on chromosome 7 (refseq:NC_000007.14, GRCh38); 1-based, inclusive interval notation."
},
{
"name": "GRCh38 0-based, half-open interval",
"value": "chr7:140753336-140753337",
"description": "Genomic positions 140,753,336 to 140,753,337 on chromosome 7 (refseq:NC_000007.14, GRCh38); 0-based, half-open interval notation."
}
],
"type": "SequenceLocation",
"digest": "1ReS370wzmC9PGTn13XrnG8Ot7UAKYuw",
"sequenceReference": {
"id": "refseq:NM_004333.6",
"name": "NM_004333.6",
"description": "The MANE Select (GRCh38) coding transcript for BRAF.",
"aliases": [
"ga4gh:SQ.aKMPEJgmlZXt_F6gRY5cUG3THH2n-GUa"
],
"type": "SequenceReference",
"refgetAccession": "SQ.aKMPEJgmlZXt_F6gRY5cUG3THH2n-GUa",
"residueAlphabet": "na"
},
"start": 2024,
"end": 2025,
"sequence": "G"
},
"state": {
"type": "LiteralSequenceExpression",
"sequence": "A"
}
},
{
"id": "ga4gh:VA.t97D17VsbiAa2U-znA-Qfx6DVInBd-_-",
"type": "Allele",
"name": "NM_004333.6:c.1798_1799delinsAG",
"description": "VRS variation of NM_004333.6:c.1799T>A, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "t97D17VsbiAa2U-znA-Qfx6DVInBd-_-",
"expressions": [
{
"syntax": "hgvs.c",
"value": "NM_004333.6:c.1798_1799delinsAG"
}
],
"location": {
"id": "ga4gh:SL.SXY8ShFrBAfSvtO_sXLMQKN3Ozc5awgh",
"description": "Coding DNA (cDNA) positions 1798 to 1799 of the BRAF MANE Select coding transcript (refseq:NM_004333.6), corresponding to genomic positions 140753336 to 140753337 on chromosome 7 (refseq:NC_000007.14, GRCh38).",
"extensions": [
{
"name": "GRCh38 1-based, inclusive interval",
"value": "chr7:140753336-140753337",
"description": "Genomic positions 140,753,336 to 140,753,337 on chromosome 7 (refseq:NC_000007.14, GRCh38); 1-based, inclusive interval notation."
},
{
"name": "GRCh38 0-based, half-open interval",
"value": "chr7:140753335-140753337",
"description": "Genomic positions 140,753,335 to 140,753,337 on chromosome 7 (refseq:NC_000007.14, GRCh38); 0-based, half-open interval notation."
}
],
"type": "SequenceLocation",
"digest": "SXY8ShFrBAfSvtO_sXLMQKN3Ozc5awgh",
"sequenceReference": {
"id": "refseq:NM_004333.6",
"name": "NM_004333.6",
"description": "The MANE Select (GRCh38) coding transcript for BRAF.",
"aliases": [
"ga4gh:SQ.aKMPEJgmlZXt_F6gRY5cUG3THH2n-GUa"
],
"type": "SequenceReference",
"refgetAccession": "SQ.aKMPEJgmlZXt_F6gRY5cUG3THH2n-GUa",
"residueAlphabet": "na"
},
"start": 2023,
"end": 2025,
"sequence": "GT"
},
"state": {
"type": "LiteralSequenceExpression",
"sequence": "AG"
}
}
]
}
Full example: YAML