GRCh38/hg38 7p22.1(chr7:5905831-6014161)x3 (copy count)
Source
ClinVar variation 151061: GRCh38/hg38 7p22.1(chr7:5905831-6014161)x3
Recipes that this example satisfies:
Properties
id: clinvar:151061ClinVar Variation ID, 151061 is the Variation ID listed within the Identifiers section of ClinVar’s Variant Details.
type: CategoricalVariantThis value is required by the specification for all Categorical Variant objects.
name: GRCh38/hg38 7p22.1(chr7:5905831-6014161)x3Human-readable label listed within the Identifiers section of ClinVar’s Variant Details.
description: An optional field to describe this Categorical Variant.This field was populated with an example value because ClinVar does not provide a longform description.
aliases: 2 HGVS expressionsAll listed HGVS representations within ClinVar’s Variant Details for the variant, including the GRCh38 (NC_000007.14) and GRCh37 (NC_000007.13) genomic representations.
extensions: cytogenetic location, clinvar variation type, and hgvs listThe 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: ClinVar and dbVarMappings 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
copiesfield 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. ThematchCharacteristicis 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)
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 (copy count)",
"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
id: clinvar:151061
type: CategoricalVariant
name: GRCh38/hg38 7p22.1(chr7:5905831-6014161)x3 (copy count)
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