GRCh38 Xp22.31(chrX:6978350-7594949)x3
Source: ClinGen CACN42032202
Recipes that this example satisfies: Categorical CNV
Attributes
id: clingen:cacn42032202, where CACN42032202 is the Canonical CNV Identifier listed by ClinGen.type: CategoricalVariant, as required by the specification.name: GRCh38 Xp22.31(chrX:6978350-7594949)x3, the Community Standard Title listed for the variant by ClinGen.description: A brief placeholder note, as ClinGen does not contain a longform description of this variant.aliases: The HGVS representations for GRCh38 (NC_000023.11) and GRCh37 (NC_000023.10) are listed.extensions: The cytogenetic location (Xp22.31) was obtained from the Community Standard Title for this variant.mappings: A mapping to ClinGen’s webpage for this variant is included.
Constraints
Copy Count Constraint: The copies field is set to 3, reflecting the “x3” copy count specified in the variant name as provided by ClinGen.
Defining Location Constraint: The defining location is a VRS Sequence Location on chromosome X (refseq:NC_000023.11, GRCh38), extracted from the GRCh38 CopyNumberCount included within members. Unlike categoricalCnv-ex1 and categoricalCnv-ex2, this example uses ranged values for both the start and end positions to reflect uncertainty in the breakpoint locations, specifying start within the interval 6,978,350–6,996,235 and end within 7,564,455–7,594,949.
Members
The members field includes one VRS CopyNumberCount object generated using the VICC Variation Normalizer: NC_000023.11:g.(6978350_6996235)_(7564455_7594949)dup on the GRCh38 chromosome X reference sequence, with a copies value of 3 and ranged start and end positions reflecting breakpoint uncertainty.
Full example: JSON
{
"id": "clingen:cacn42032202",
"type": "CategoricalVariant",
"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
}
]
}
Full example: YAML