NC_000001.11:g.1699974C>G
Source
Recipes that this example satisfies
Properties
id: clingen:CA415424538CA415424538 is the Canonical Allele Identifier listed by ClinGen.
type: CategoricalVariantThis value is required by the specification for all Categorical Variant objects.
name: NC_000001.11:g.1699974C>GThe GRCh38 HGVS Genomic Allele listed for the variant by ClinGen.
description: An example canonical allele.This field was populated with an example value because ClinGen does not provide a longform description.
aliases: 2 HGVS expressions.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: cytogenetic location and hgvs listThe 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: ClinGen, dbSNP, gnomAD (v2, v3, and v4)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.
- Defining Allele Constraint
The
allelefield is populated with the VRS Allele corresponding to the GRCh38 genomic representation NC_000001.11:g.1699974C>G, as included withinmembers. 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
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