{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA122886", "communityStandardTitle": [ "NM_000448.3(RAG1):c.1682G>A (p.Arg561His)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=28182[alleleid]", "alleleId": 28182, "preferredName": "NM_000448.3(RAG1):c.1682G>A (p.Arg561His)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/13143", "RCV": [ "RCV000014025", "RCV001384043", "RCV001332464", "RCV001781262", "RCV003473089" ], "variationId": 13143 } ], "ExAC": [ { "@id": "http://exac.broadinstitute.org/variant/11-36596536-G-A", "id": "11-36596536-G-A", "variant": "11:36596536 G / A" } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr11:g.36596536G>A?assembly=hg19", "id": "chr11:g.36596536G>A" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr11:g.36574986G>A?assembly=hg38", "id": "chr11:g.36574986G>A" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/104894284", "rs": 104894284 } ], "gnomAD_2": [ { "@id": "http://gnomad.broadinstitute.org/variant/11-36596536-G-A?dataset=gnomad_r2_1", "id": "11-36596536-G-A", "variant": "11:36596536 G / A" } ], "gnomAD_3": [ { "@id": "http://gnomad.broadinstitute.org/variant/11-36574986-G-A?dataset=gnomad_r3", "id": "11-36574986-G-A", "variant": "11:36574986 G / A" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/11-36574986-G-A?dataset=gnomad_r4", "id": "11-36574986-G-A", "variant": "11:36574986 G / A" } ] }, "genomicAlleles": [ { "chromosome": "11", "coordinates": [ { "allele": "A", "end": 36574986, "referenceAllele": "G", "start": 36574985 } ], "hgvs": [ "NC_000011.10:g.36574986G>A", "CM000673.2:g.36574986G>A" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000059" }, { "chromosome": "11", "coordinates": [ { "allele": "A", "end": 36596536, "referenceAllele": "G", "start": 36596535 } ], "hgvs": [ "NC_000011.9:g.36596536G>A", "CM000673.1:g.36596536G>A" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000035" }, { "chromosome": "11", "coordinates": [ { "allele": "A", "end": 36553112, "referenceAllele": "G", "start": 36553111 } ], "hgvs": [ "NC_000011.8:g.36553112G>A" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000011" }, { "coordinates": [ { "allele": "A", "end": 11974, "referenceAllele": "G", "start": 11973 } ], "hgvs": [ "NG_007528.1:g.11974G>A", "LRG_98:g.11974G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS000636" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 1978, "referenceAllele": "G", "start": 1977 } ], "gene": "http://reg.genome.network/gene/GN009831", "geneNCBI_id": 5896, "geneSymbol": "RAG1", "hgvs": [ "ENST00000697713.1:c.1682G>A" ], "proteinEffect": { "hgvs": "ENSP00000513411.1:p.Arg561His", "hgvsWellDefined": "ENSP00000513411.1:p.Arg561His" }, "referenceSequence": "http://reg.genome.network/refseq/RS908925" }, { "coordinates": [ { "allele": "A", "end": 1862, "referenceAllele": "G", "start": 1861 } ], "gene": "http://reg.genome.network/gene/GN009831", "geneNCBI_id": 5896, "geneSymbol": "RAG1", "hgvs": [ "ENST00000697714.1:c.1682G>A" ], "proteinEffect": { "hgvs": "ENSP00000513412.1:p.Arg561His", "hgvsWellDefined": "ENSP00000513412.1:p.Arg561His" }, "referenceSequence": "http://reg.genome.network/refseq/RS908926" }, { "coordinates": [ { "allele": "A", "end": 2105, "referenceAllele": "G", "start": 2104 } ], "gene": "http://reg.genome.network/gene/GN009831", "geneNCBI_id": 5896, "geneSymbol": "RAG1", "hgvs": [ "ENST00000697715.1:c.1682G>A" ], "proteinEffect": { "hgvs": "ENSP00000513413.1:p.Arg561His", "hgvsWellDefined": "ENSP00000513413.1:p.Arg561His" }, "referenceSequence": "http://reg.genome.network/refseq/RS908927" }, { "coordinates": [ { "allele": "A", "end": 1812, "referenceAllele": "G", "start": 1811 } ], "gene": "http://reg.genome.network/gene/GN009831", "geneNCBI_id": 5896, "geneSymbol": "RAG1", "hgvs": [ "ENST00000299440.6:c.1682G>A" ], "proteinEffect": { "hgvs": "ENSP00000299440.5:p.Arg561His", "hgvsWellDefined": "ENSP00000299440.5:p.Arg561His" }, "referenceSequence": "http://reg.genome.network/refseq/RS744676", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000299440.6:c.1682G>A" }, "RefSeq": { "hgvs": "NM_000448.3:c.1682G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000299440.5:p.Arg561His" }, "RefSeq": { "hgvs": "NP_000439.2:p.Arg561His" } } } }, { "coordinates": [ { "allele": "A", "end": 1794, "referenceAllele": "G", "start": 1793 } ], "gene": "http://reg.genome.network/gene/GN009831", "geneNCBI_id": 5896, "geneSymbol": "RAG1", "hgvs": [ "ENST00000299440.5:c.1682G>A" ], "proteinEffect": { "hgvs": "ENSP00000299440.5:p.Arg561His", "hgvsWellDefined": "ENSP00000299440.5:p.Arg561His" }, "referenceSequence": "http://reg.genome.network/refseq/RS254725" }, { "coordinates": [ { "allele": "A", "end": 2318, "referenceAllele": "G", "start": 2317 } ], "gene": "http://reg.genome.network/gene/GN009831", "geneNCBI_id": 5896, "geneSymbol": "RAG1", "hgvs": [ "ENST00000534663.1:c.1682G>A" ], "proteinEffect": { "hgvs": "ENSP00000434610.1:p.Arg561His", "hgvsWellDefined": "ENSP00000434610.1:p.Arg561His" }, "referenceSequence": "http://reg.genome.network/refseq/RS359238" }, { "@id": "http://reg.genome.network/allele/PA122888", "coordinates": [ { "allele": "A", "end": 1806, "referenceAllele": "G", "start": 1805 } ], "gene": "http://reg.genome.network/gene/GN009831", "geneNCBI_id": 5896, "geneSymbol": "RAG1", "hgvs": [ "NM_000448.2:c.1682G>A", "LRG_98t1:c.1682G>A" ], "proteinEffect": { "hgvs": "NP_000439.1:p.Arg561His", "hgvsWellDefined": "NP_000439.1:p.Arg561His" }, "referenceSequence": "http://reg.genome.network/refseq/RS006510" }, { "coordinates": [ { "allele": "A", "end": 1834, "referenceAllele": "G", "start": 1833 } ], "gene": "http://reg.genome.network/gene/GN009831", "geneNCBI_id": 5896, "geneSymbol": "RAG1", "hgvs": [ "XM_005253041.3:c.1682G>A" ], "proteinEffect": { "hgvs": "XP_005253098.1:p.Arg561His", "hgvsWellDefined": "XP_005253098.1:p.Arg561His" }, "referenceSequence": "http://reg.genome.network/refseq/RS060133" }, { "coordinates": [ { "allele": "A", "end": 1948, "referenceAllele": "G", "start": 1947 } ], "gene": "http://reg.genome.network/gene/GN009831", "geneNCBI_id": 5896, "geneSymbol": "RAG1", "hgvs": [ "XM_011520250.1:c.1682G>A" ], "proteinEffect": { "hgvs": "XP_011518552.1:p.Arg561His", "hgvsWellDefined": "XP_011518552.1:p.Arg561His" }, "referenceSequence": "http://reg.genome.network/refseq/RS087419" }, { "coordinates": [ { "allele": "A", "end": 2046, "referenceAllele": "G", "start": 2045 } ], "gene": "http://reg.genome.network/gene/GN009831", "geneNCBI_id": 5896, "geneSymbol": "RAG1", "hgvs": [ "XM_011520251.1:c.1682G>A" ], "proteinEffect": { "hgvs": "XP_011518553.1:p.Arg561His", "hgvsWellDefined": "XP_011518553.1:p.Arg561His" }, "referenceSequence": "http://reg.genome.network/refseq/RS087420" }, { "coordinates": [ { "allele": "A", "end": 1868, "referenceAllele": "G", "start": 1867 } ], "gene": "http://reg.genome.network/gene/GN009831", "geneNCBI_id": 5896, "geneSymbol": "RAG1", "hgvs": [ "XM_005253041.4:c.1682G>A" ], "proteinEffect": { "hgvs": "XP_005253098.1:p.Arg561His", "hgvsWellDefined": "XP_005253098.1:p.Arg561His" }, "referenceSequence": "http://reg.genome.network/refseq/RS533889" }, { "coordinates": [ { "allele": "A", "end": 1982, "referenceAllele": "G", "start": 1981 } ], "gene": "http://reg.genome.network/gene/GN009831", "geneNCBI_id": 5896, "geneSymbol": "RAG1", "hgvs": [ "XM_011520250.2:c.1682G>A" ], "proteinEffect": { "hgvs": "XP_011518552.1:p.Arg561His", "hgvsWellDefined": "XP_011518552.1:p.Arg561His" }, "referenceSequence": "http://reg.genome.network/refseq/RS545657" }, { "@id": "http://reg.genome.network/allele/PA2825177491", "coordinates": [ { "allele": "A", "end": 1812, "referenceAllele": "G", "start": 1811 } ], "gene": "http://reg.genome.network/gene/GN009831", "geneNCBI_id": 5896, "geneSymbol": "RAG1", "hgvs": [ "NM_000448.3:c.1682G>A" ], "proteinEffect": { "hgvs": "NP_000439.2:p.Arg561His", "hgvsWellDefined": "NP_000439.2:p.Arg561His" }, "referenceSequence": "http://reg.genome.network/refseq/RS674851", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000299440.6:c.1682G>A" }, "RefSeq": { "hgvs": "NM_000448.3:c.1682G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000299440.5:p.Arg561His" }, "RefSeq": { "hgvs": "NP_000439.2:p.Arg561His" } } } }, { "@id": "http://reg.genome.network/allele/PA2828706846", "coordinates": [ { "allele": "A", "end": 2155, "referenceAllele": "G", "start": 2154 } ], "gene": "http://reg.genome.network/gene/GN009831", "geneNCBI_id": 5896, "geneSymbol": "RAG1", "hgvs": [ "NM_001377277.1:c.1682G>A" ], "proteinEffect": { "hgvs": "NP_001364206.1:p.Arg561His", "hgvsWellDefined": "NP_001364206.1:p.Arg561His" }, "referenceSequence": "http://reg.genome.network/refseq/RS695063" }, { "@id": "http://reg.genome.network/allele/PA2828707528", "coordinates": [ { "allele": "A", "end": 2093, "referenceAllele": "G", "start": 2092 } ], "gene": "http://reg.genome.network/gene/GN009831", "geneNCBI_id": 5896, "geneSymbol": "RAG1", "hgvs": [ "NM_001377278.1:c.1682G>A" ], "proteinEffect": { "hgvs": "NP_001364207.1:p.Arg561His", "hgvsWellDefined": "NP_001364207.1:p.Arg561His" }, "referenceSequence": "http://reg.genome.network/refseq/RS695064" }, { "@id": "http://reg.genome.network/allele/PA2828708208", "coordinates": [ { "allele": "A", "end": 1995, "referenceAllele": "G", "start": 1994 } ], "gene": "http://reg.genome.network/gene/GN009831", "geneNCBI_id": 5896, "geneSymbol": "RAG1", "hgvs": [ "NM_001377279.1:c.1682G>A" ], "proteinEffect": { "hgvs": "NP_001364208.1:p.Arg561His", "hgvsWellDefined": "NP_001364208.1:p.Arg561His" }, "referenceSequence": "http://reg.genome.network/refseq/RS695065" }, { "@id": "http://reg.genome.network/allele/PA2573074412", "coordinates": [ { "allele": "A", "end": 1881, "referenceAllele": "G", "start": 1880 } ], "gene": "http://reg.genome.network/gene/GN009831", "geneNCBI_id": 5896, "geneSymbol": "RAG1", "hgvs": [ "NM_001377280.1:c.1682G>A" ], "proteinEffect": { "hgvs": "NP_001364209.1:p.Arg561His", "hgvsWellDefined": "NP_001364209.1:p.Arg561His" }, "referenceSequence": "http://reg.genome.network/refseq/RS695066" } ], "type": "nucleotide" }