GRCh38/hg38 7p22.1(chr7:5905831-6014161)x3
Source: ClinVar variation 151061: GRCh38/hg38 7p22.1(chr7:5905831-6014161)x3
Recipes that this example satisfies: Categorical CNV
Attributes
id: clinvar:151061, where 151061 is the Variation ID listed within the Identifiers section of ClinVar’s Variant Details.type: CategoricalVariant, as required by the specification.name: GRCh38/hg38 7p22.1(chr7:5905831-6014161)x3, 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: All listed HGVS representations within ClinVar’s Variant Details for the variant: the GRCh38 (NC_000007.14) and GRCh37 (NC_000007.13) genomic representations.extensions: The cytogenetic location (7p22.1) and ClinVar variation type (copy number gain) are obtained from ClinVar’s Variant Details. The hgvs list extension includes the GRCh38 and GRCh37 HGVS genomic representations.mappings: Mappings to ClinVar’s page for the variant and dbVar are included from the Links section of ClinVar’s Variant Details.
Constraints
Copy Count Constraint: The copies field is set to 3, reflecting the “x3” copy count specified in the variant name as provided by ClinVar.
Defining Location Constraint: The defining location is a VRS Sequence Location on chromosome 7 (refseq:NC_000007.14, GRCh38) spanning positions 5,905,831 to 6,014,161, extracted from the GRCh38 CopyNumberCount included within members. The matchCharacteristic is set to is_within, and a liftover relation is included to link the GRCh38 and GRCh37 representations.
Members
The members field includes two VRS CopyNumberCount objects generated using the VICC Variation Normalizer from the HGVS representations of this variant: NC_000007.14:g.(?_5905831)_(6014161_?)dup (GRCh38) and NC_000007.13:g.(?_5945462)_(6053792_?)dup (GRCh37). Both members have a copies value of 3.
Full example: JSON
{
"id": "clinvar:151061",
"type": "CategoricalVariant",
"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
}
]
}
Full example: YAML