NM_007294.4(BRCA1):c.5558dup (p.Tyr1853Ter)
Source: ClinVar variation 55628: NM_007294.4(BRCA1):c.5558dup (p.Tyr1853Ter)
Recipes that this example satisfies: Protein Sequence Consequence
Attributes
id: clinvar:55628, where 55628 is the Variation ID listed within the Identifiers section of ClinVar’s Variant Details.type: CategoricalVariant, as required by the specification.name: NM_007294.4(BRCA1):c.5558dup (p.Tyr1853Ter), the human-readable label listed within the Identifiers section of ClinVar’s Variant Details.description: A brief placeholder note, as ClinVar does not contain a longform description of this variant.aliases: A subset of HGVS representations from ClinVar’s Variant Details, including the MANE Select nucleotide coding (NM_007294.4:c.5558dup) and protein expressions (NP_009225.1:p.Tyr1853Ter and NP_009225.1:p.Y1853*), the full HGVS name with single-letter amino acid abbreviation, and both GRCh38 and GRCh37 hgvs.g variants, as well as the Canonical SPDI representation provided by ClinVar.extensions: The cytogenetic location (17q21.31) and ClinVar variation type (Duplication) are obtained from ClinVar’s Variant Details. The hgvs list extension includes GRCh38 genomic, GRCh37 genomic, MANE Select coding, and protein HGVS representations.mappings: Mappings to ClinVar’s page for the variant, ClinGen, and dbSNP are included from the Links section of ClinVar’s Variant Details.
Constraints
Defining Allele Constraint: The allele field is populated with the VRS Allele corresponding to the MANE Select protein representation NP_009225.1:p.Tyr1853Ter, as included within members. The constraint includes a translation_of relation linking the protein allele to its coding DNA representation.
Members
The members field includes three VRS Allele objects generated using the VICC Variation Normalizer: NC_000017.11:g.43045712dup (GRCh38 genomic, on refseq:NC_000017.11), NC_000017.10:g.41197729dup (GRCh37 genomic, on refseq:NC_000017.10), and NP_009225.1:p.Tyr1853Ter (protein, on the MANE Select protein product for BRCA1 refseq:NP_009225.1). The variant normalization service was unable to generate a VRS Allele for the MANE Select coding representation NM_007294.4:c.5558dup.
Full example: JSON
{
"id": "clinvar:55628",
"type": "CategoricalVariant",
"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": "*"
}
}
]
}
Full example: YAML