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canonicalAllele-ex1.yaml
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id: clinvar:662001
type: CategoricalVariant
name: NM_004958.4(MTOR):c.5992_5993del (p.Met1998fs)
description: ...
aliases:
- NM_004958.4:c.5992_5993del
- NC_000001.11:g.11128044_11128045del
- NC_000001.10:g.11188101_11188102del
- NP_004949.3:p.Met1998fs
- NG_033239.1:g.139507_139508del
- LRG_734:g.139507_139508del
- LRG_734t1:c.5992_5993del
extensions:
- name: cytogenetic location
value: 1p36.22
- name: clinvar variation type
value: Deletion
- name: hgvs list
value:
- nucleotideExpression:
syntax: hgvs.g
value: NC_000001.11:g.11128044_11128045del
nucleotideType: genomic
- nucleotideExpression:
syntax: hgvs.c
value: NM_004958.4:c.5992_5993del
nucleotideType: coding
maneSelect: true
proteinExpression:
syntax: hgvs.p
value: NP_004949.3:p.Met1998fs
molecularConsequence:
name: frameshift_variant
system: http://www.sequenceontology.org/browser/
systemVersion: release_2.5.3
code: SO:0001589
iris:
- http://www.sequenceontology.org/browser/release_2.5.3/term/SO:0001589
- nucleotideExpression:
syntax: hgvs.g
value: NG_033239.1:g.139507_139508del
nucleotideType: genomic
- nucleotideExpression:
syntax: hgvs.g
value: LRG_734:g.139507_139508del
nucleotideType: genomic
- nucleotideExpression:
syntax: hgvs.c
value: LRG_734t1:c.5992_5993del
nucleotideType: coding
constraints:
- type: DefiningAlleleConstraint
allele:
id: ga4gh:VA.0TMQdMT2OBisJ9FI4tkzaBtxGB7r8FfJ
type: Allele
name: NM_004958.4:c.5992_5993del
description: VRS variation of NC_000001.11:g.11128044_11128045del, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).
extensions:
- name: clinvar vcf
value: 1-11128043-CAT-C
digest: 0TMQdMT2OBisJ9FI4tkzaBtxGB7r8FfJ
expressions:
- syntax: spdi
value: 'NC_000001.11:11128043:AT:'
- syntax: hgvs.g
value: NC_000001.11:g.11128044_11128045del
- syntax: hgvs.c
value: NM_004958.4:c.5992_5993del
- syntax: hgvs.p
value: NP_004949.1:p.Met1998fs
location:
id: ga4gh:SL.gLe4d4Seuxn5fLCfO_2g34gF86vpGvo1
type: SequenceLocation
digest: gLe4d4Seuxn5fLCfO_2g34gF86vpGvo1
sequenceReference:
type: SequenceReference
refgetAccession: SQ.QheGYEnKbwNpM3LulbPTBQhyBSyZwuYm
start: 6112
end: 6114
sequence: AT
state:
type: ReferenceLengthExpression
length: 0
sequence: ''
repeatSubunitLength: 2
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://www.ncbi.nlm.nih.gov/clinvar
code: '662001'
iris:
- https://www.ncbi.nlm.nih.gov/clinvar/variation/662001
relation: exactMatch
- coding:
system: https://reg.clinicalgenome.org
code: CA915941124
iris:
- https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA915941124
relation: relatedMatch
- coding:
system: https://varsome.com
code: hg38/rs1570942058
iris:
- https://varsome.com/variant/hg38/rs1570942058
relation: relatedMatch
- coding:
system: https://www.ncbi.nlm.nih.gov/snp
code: rs1570942058
iris:
- https://www.ncbi.nlm.nih.gov/snp/rs1570942058
relation: relatedMatch
members:
- id: ga4gh:VA.PN-6_l2_yI1UPBRCtFnWkR52iZXKVJ8b
type: Allele
name: NC_000001.11:g.11128044_11128045del
description: VRS variation of NC_000001.11:g.11128044_11128045del, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).
extensions:
- name: clinvar_vcf
value: 1-11128043-CAT-C
digest: PN-6_l2_yI1UPBRCtFnWkR52iZXKVJ8b
expressions:
- syntax: spdi
value: 'NC_000001.11:11128043:AT:'
- syntax: hgvs.g
value: NC_000001.11:g.11128044_11128045del
- syntax: hgvs.c
value: NM_004958.4:c.5992_5993del
- syntax: hgvs.p
value: NP_004949.1:p.Met1998fs
location:
id: ga4gh:SL.5-SKfXZ941W7JbZW3UmQKtijyUfd6d7z
type: SequenceLocation
digest: 5-SKfXZ941W7JbZW3UmQKtijyUfd6d7z
sequenceReference:
type: SequenceReference
refgetAccession: SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO
start: 11128043
end: 11128045
sequence: AT
state:
type: ReferenceLengthExpression
length: 0
sequence: ''
repeatSubunitLength: 2
- id: ga4gh:VA.0TMQdMT2OBisJ9FI4tkzaBtxGB7r8FfJ
type: Allele
name: NM_004958.4:c.5992_5993del
description: VRS variation of NM_004958.4:c.5992_5993del, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).
extensions:
- name: clinvar vcf
value: 1-11128043-CAT-C
digest: 0TMQdMT2OBisJ9FI4tkzaBtxGB7r8FfJ
expressions:
- syntax: spdi
value: 'NC_000001.11:11128043:AT:'
- syntax: hgvs.g
value: NC_000001.11:g.11128044_11128045del
- syntax: hgvs.c
value: NM_004958.4:c.5992_5993del
- syntax: hgvs.p
value: NP_004949.1:p.Met1998fs
location:
id: ga4gh:SL.gLe4d4Seuxn5fLCfO_2g34gF86vpGvo1
type: SequenceLocation
digest: gLe4d4Seuxn5fLCfO_2g34gF86vpGvo1
sequenceReference:
type: SequenceReference
refgetAccession: SQ.QheGYEnKbwNpM3LulbPTBQhyBSyZwuYm
start: 6112
end: 6114
sequence: AT
state:
type: ReferenceLengthExpression
length: 0
sequence: ''
repeatSubunitLength: 2