Categorical CNV
Definition and Information Model
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
A CategoricalCNV is a Categorical Variant with exactly two constraints:
A Defining Location Constraint with the .relations array containing only a liftover_to code.
Examples
The following are example implementations of that satisfy the CanonicalAllele 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"
}