NC_000001.11:g.1699974C>G
Source: ClinGen CA415424538
Recipes that this example satisfies: Canonical Allele
Attributes
id: clingen:CA415424538, where CA415424538 is the Canonical Allele Identifier listed by ClinGen.type: CategoricalVariant, as required by the specification.name: NC_000001.11:g.1699974C>G, the GRCh38 HGVS Genomic Allele 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 of genomic alleles for GRCh38 (NC_000001.11:g.1699974C>G) and GRCh37 (NC_000001.10:g.1631413C>G), as provided by ClinGen.extensions: The cytogenetic location (1p36.33) was obtained from the HGNC pages for MMP23A (HGNC:7170) and MMP23B (HGNC:7171), the genes listed for this Canonical Allele. The hgvs list extension includes the hgvs.g representations for GRCh38 and GRCh37.mappings: Mappings to ClinGen’s webpage, dbSNP, and gnomAD v2, v3, and v4 are included from the Linked Data section of ClinGen’s page for this Canonical Allele.
Constraints
Defining Allele Constraint: The allele field is populated with the VRS Allele corresponding to the GRCh38 genomic representation NC_000001.11:g.1699974C>G, as included within members. The constraint includes relations specifying liftover and transcription relationships between the alleles.
Members
The members field includes two VRS Allele objects generated using the VICC Variation Normalizer from the hgvs.g representations of this variant on GRCh38 (NC_000001.11:g.1699974C>G) and GRCh37 (NC_000001.10:g.1631413C>G), respectively.
Full example: JSON
{
"id": "clingen:CA415424538",
"type": "CategoricalVariant",
"name": "NC_000001.11:g.1699974C>G",
"description": "An example canonical allele.",
"aliases": [
"NC_000001.11:g.1699974C>G",
"NC_000001.10:g.1631413C>G"
],
"extensions": [
{
"name": "cytogenetic location",
"value": "1p36.33"
},
{
"name": "hgvs list",
"value": [
{
"nucleotideExpression": {
"syntax": "hgvs.g",
"value": "NC_000001.11:g.1699974C>G"
}
},
{
"nucleotideExpression": {
"syntax": "hgvs.g",
"value": "NC_000001.10:g.1631413C>G"
}
}
]
}
],
"constraints": [
{
"type": "DefiningAlleleConstraint",
"allele": {
"id": "ga4gh:VA.WjRY1EXgci6Nd0M2yI86Ue_OOnfnb-Ss",
"type": "Allele",
"name": "NC_000001.11:g.1699974C>G",
"description": "VRS Allele of NC_000001.11:g.1699974C>G, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "WjRY1EXgci6Nd0M2yI86Ue_OOnfnb-Ss",
"expressions": [
{
"syntax": "hgvs.g",
"value": "NC_000001.11:g.1699974C>G"
}
],
"location": {
"id": "ga4gh:SL.YmbtK6FLqlk2bLjpFwH-y7k4RLq_t7L3",
"description": "Genomic position 1699974 on chromosome 1 (refseq:NC_000001.11, GRCh38).",
"extensions": [
{
"name": "GRCh38 1-based, genomic position",
"value": "chr1:1699974",
"description": "Genomic position 1,699,974 on chromosome 1 (refseq:NC_000001.11, GRCh38)."
},
{
"name": "GRCh38 1-based, inclusive interval notation",
"value": "chr1:1699974-1699974",
"description": "Genomic positions 1,699,974 to 1,699,974 on chromosome 1 (refseq:NC_000001.11, GRCh38); 1-based, inclusive interval notation."
},
{
"name": "GRCh38 0-based, half-open interval notation",
"value": "chr1:1699973-1699974",
"description": "Genomic positions 1,699,973 to 1,699,974 on chromosome 1 (refseq:NC_000001.11, GRCh38); 0-based, half-open interval notation."
}
],
"type": "SequenceLocation",
"digest": "YmbtK6FLqlk2bLjpFwH-y7k4RLq_t7L3",
"sequenceReference": {
"id": "refseq:NC_000001.11",
"name": "NC_000001.11",
"description": "Reference sequence for GRCh38 chromosome 1.",
"aliases": [
"GRCh38:1",
"GRCh38:chr1",
"ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO"
],
"type": "SequenceReference",
"refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
"residueAlphabet": "na"
},
"start": 1699973,
"end": 1699974,
"sequence": "C"
},
"state": {
"type": "LiteralSequenceExpression",
"sequence": "G"
}
},
"relations": [
{
"primaryCoding": {
"code": "liftover_to",
"system": "ga4gh-gks-term:allele-relation"
}
},
{
"primaryCoding": {
"code": "transcribed_to",
"system": "http://www.sequenceontology.org",
"iris": [
"http://www.sequenceontology.org/browser/current_release/term/transcribed_to"
]
}
}
]
}
],
"mappings": [
{
"coding": {
"system": "https://reg.clinicalgenome.org/",
"code": "CA415424538",
"iris": [
"https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA415424538"
]
},
"relation": "exactMatch"
},
{
"coding": {
"system": "https://www.ncbi.nlm.nih.gov/snp/",
"code": "rs1391950675",
"iris": [
"https://www.ncbi.nlm.nih.gov/snp/rs1391950675"
]
},
"relation": "relatedMatch"
},
{
"coding": {
"system": "https://gnomad.broadinstitute.org",
"code": "1-1631413-C-G",
"iris": [
"https://gnomad.broadinstitute.org/variant/1-1631413-C-G?dataset=gnomad_r2_1"
],
"extensions": [
{
"name": "dataset",
"value": "gnomad_r2_1"
}
]
},
"relation": "relatedMatch"
},
{
"coding": {
"system": "https://gnomad.broadinstitute.org",
"code": "1-1699974-C-G",
"iris": [
"https://gnomad.broadinstitute.org/variant/1-1699974-C-G?dataset=gnomad_r3"
],
"extensions": [
{
"name": "dataset",
"value": "gnomad_r3"
}
]
},
"relation": "relatedMatch"
},
{
"coding": {
"system": "https://gnomad.broadinstitute.org",
"code": "chr1-1699974-C-G",
"iris": [
"https://gnomad.broadinstitute.org/variant/chr1-1699974-C-G?dataset=gnomad_r4"
],
"extensions": [
{
"name": "dataset",
"value": "gnomad_r4"
}
]
},
"relation": "relatedMatch"
}
],
"members": [
{
"id": "ga4gh:VA.WjRY1EXgci6Nd0M2yI86Ue_OOnfnb-Ss",
"type": "Allele",
"name": "NC_000001.11:g.1699974C>G",
"description": "VRS variation of NC_000001.11:g.1699974C>G, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "WjRY1EXgci6Nd0M2yI86Ue_OOnfnb-Ss",
"expressions": [
{
"syntax": "hgvs.g",
"value": "NC_000001.11:g.1699974C>G"
}
],
"location": {
"id": "ga4gh:SL.YmbtK6FLqlk2bLjpFwH-y7k4RLq_t7L3",
"description": "Genomic position 1,699,974 on chromosome 1 (refseq:NC_000001.11, GRCh38).",
"type": "SequenceLocation",
"extensions": [
{
"name": "GRCh38 1-based, genomic position",
"value": "chr1:1699974",
"description": "Genomic position 1,699,974 on chromosome 1 (refseq:NC_000001.11, GRCh38)."
},
{
"name": "GRCh38 1-based, inclusive interval notation",
"value": "chr1:1699974-1699974",
"description": "Genomic positions 1,699,974 to 1,699,974 on chromosome 1 (refseq:NC_000001.11, GRCh38); 1-based, inclusive interval notation."
},
{
"name": "GRCh38 0-based, half-open interval notation",
"value": "chr1:1699973-1699974",
"description": "Genomic positions 1,699,973 to 1,699,974 on chromosome 1 (refseq:NC_000001.11, GRCh38); 0-based, half-open interval notation."
}
],
"digest": "YmbtK6FLqlk2bLjpFwH-y7k4RLq_t7L3",
"sequenceReference": {
"id": "refseq:NC_000001.11",
"name": "NC_000001.11",
"description": "Reference sequence for GRCh38 chromosome 1.",
"aliases": [
"GRCh38:1",
"GRCh38:chr1",
"ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO"
],
"type": "SequenceReference",
"refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
"residueAlphabet": "na"
},
"start": 1699973,
"end": 1699974,
"sequence": "C"
},
"state": {
"type": "LiteralSequenceExpression",
"sequence": "G"
}
},
{
"id": "ga4gh:VA.WW0r6Dh-z_ftn9yS-i0f1Y62JNCpVed2",
"type": "Allele",
"name": "NC_000001.10:g.1631413C>G",
"description": "VRS variation of NC_000001.10:g.1631413C>G, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "WW0r6Dh-z_ftn9yS-i0f1Y62JNCpVed2",
"expressions": [
{
"syntax": "hgvs.g",
"value": "NC_000001.10:g.1631413C>G"
}
],
"location": {
"id": "ga4gh:SL.QsC4TgLsfR6-TatBj1sVKAgfv9bGYSxb",
"description": "Genomic position 1,631,413 on chromosome 1 (refseq:NC_000001.10, GRCh37).",
"type": "SequenceLocation",
"extensions": [
{
"name": "GRCh37 1-based, genomic position",
"value": "chr1:1631413",
"description": "Genomic position 1,631,413 on chromosome 1 (refseq:NC_000001.10, GRCh37)."
},
{
"name": "GRCh37 1-based, inclusive interval notation",
"value": "chr1:1631413-1631413",
"description": "Genomic positions 1,631,413 to 1,631,413 on chromosome 1 (refseq:NC_000001.10, GRCh37); 1-based, inclusive interval notation."
},
{
"name": "GRCh37 0-based, half-open interval notation",
"value": "chr1:1631412-1631413",
"description": "Genomic positions 1,631,412 to 1,631,413 on chromosome 1 (refseq:NC_000001.10, GRCh37); 0-based, half-open interval notation."
}
],
"digest": "QsC4TgLsfR6-TatBj1sVKAgfv9bGYSxb",
"sequenceReference": {
"id": "refseq:NC_000001.10",
"name": "NC_000001.10",
"description": "Reference sequence for GRCh37 chromosome 1.",
"aliases": [
"GRCh37.1",
"GRCh37:chr1",
"ga4gh:SQ.S_KjnFVz-FE7M0W6yoaUDgYxLPc1jyWU"
],
"type": "SequenceReference",
"refgetAccession": "SQ.S_KjnFVz-FE7M0W6yoaUDgYxLPc1jyWU",
"residueAlphabet": "na"
},
"start": 1631412,
"end": 1631413,
"sequence": "C"
},
"state": {
"type": "LiteralSequenceExpression",
"sequence": "G"
}
}
]
}
Full example: YAML