{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA9226292", "communityStandardTitle": [ "NM_000528.4(MAN2B1):c.1838G>A (p.Arg613Gln)" ], "externalRecords": { "COSMIC": [ { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=1189895", "active": true, "id": "COSM1189895" } ], "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=446031[alleleid]", "alleleId": 446031, "preferredName": "NM_000528.4(MAN2B1):c.1838G>A (p.Arg613Gln)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/450771", "RCV": [ "RCV000521153", "RCV001083132" ], "variationId": 450771 } ], "ExAC": [ { "@id": "http://exac.broadinstitute.org/variant/19-12763267-C-T", "id": "19-12763267-C-T", "variant": "19:12763267 C / T" } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr19:g.12763267C>T?assembly=hg19", "id": "chr19:g.12763267C>T" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr19:g.12652453C>T?assembly=hg38", "id": "chr19:g.12652453C>T" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/543222535", "rs": 543222535 } ], "gnomAD_2": [ { "@id": "http://gnomad.broadinstitute.org/variant/19-12763267-C-T?dataset=gnomad_r2_1", "id": "19-12763267-C-T", "variant": "19:12763267 C / T" } ], "gnomAD_3": [ { "@id": "http://gnomad.broadinstitute.org/variant/19-12652453-C-T?dataset=gnomad_r3", "id": "19-12652453-C-T", "variant": "19:12652453 C / T" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/19-12652453-C-T?dataset=gnomad_r4", "id": "19-12652453-C-T", "variant": "19:12652453 C / T" } ] }, "genomicAlleles": [ { "chromosome": "19", "coordinates": [ { "allele": "T", "end": 12652453, "referenceAllele": "C", "start": 12652452 } ], "hgvs": [ "NC_000019.10:g.12652453C>T", "CM000681.2:g.12652453C>T" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000067" }, { "chromosome": "19", "coordinates": [ { "allele": "T", "end": 12763267, "referenceAllele": "C", "start": 12763266 } ], "hgvs": [ "NC_000019.9:g.12763267C>T", "CM000681.1:g.12763267C>T" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000043" }, { "chromosome": "19", "coordinates": [ { "allele": "T", "end": 12624267, "referenceAllele": "C", "start": 12624266 } ], "hgvs": [ "NC_000019.8:g.12624267C>T" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000019" }, { "coordinates": [ { "allele": "A", "end": 19325, "referenceAllele": "G", "start": 19324 } ], "hgvs": [ "NG_008318.1:g.19325G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS001025" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 1879, "referenceAllele": "G", "start": 1878 } ], "gene": "http://reg.genome.network/gene/GN006826", "geneNCBI_id": 4125, "geneSymbol": "MAN2B1", "hgvs": [ "ENST00000456935.7:c.1838G>A" ], "proteinEffect": { "hgvs": "ENSP00000395473.2:p.Arg613Gln", "hgvsWellDefined": "ENSP00000395473.2:p.Arg613Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS756575", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000456935.7:c.1838G>A" }, "RefSeq": { "hgvs": "NM_000528.4:c.1838G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000395473.2:p.Arg613Gln" }, "RefSeq": { "hgvs": "NP_000519.2:p.Arg613Gln" } } } }, { "coordinates": [ { "allele": "A", "end": 1868, "referenceAllele": "G", "start": 1867 } ], "gene": "http://reg.genome.network/gene/GN006826", "geneNCBI_id": 4125, "geneSymbol": "MAN2B1", "hgvs": [ "ENST00000221363.8:c.1835G>A" ], "proteinEffect": { "hgvs": "ENSP00000221363.4:p.Arg612Gln", "hgvsWellDefined": "ENSP00000221363.4:p.Arg612Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS248273" }, { "coordinates": [ { "allele": "A", "end": 444, "referenceAllele": "G", "start": 443 } ], "gene": "http://reg.genome.network/gene/GN006826", "geneNCBI_id": 4125, "geneSymbol": "MAN2B1", "hgvs": [ "ENST00000433513.5:n.444G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS292580" }, { "coordinates": [ { "allele": "A", "end": 1879, "referenceAllele": "G", "start": 1878 } ], "gene": "http://reg.genome.network/gene/GN006826", "geneNCBI_id": 4125, "geneSymbol": "MAN2B1", "hgvs": [ "ENST00000456935.6:c.1838G>A" ], "proteinEffect": { "hgvs": "ENSP00000395473.2:p.Arg613Gln", "hgvsWellDefined": "ENSP00000395473.2:p.Arg613Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS303709" }, { "coordinates": [ { "allele": "A", "end": 2428, "referenceAllele": "G", "start": 2427 } ], "gene": "http://reg.genome.network/gene/GN006826", "geneNCBI_id": 4125, "geneSymbol": "MAN2B1", "hgvs": [ "ENST00000466794.5:n.2428G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS310063" }, { "coordinates": [ { "allele": "A", "end": 431, "referenceAllele": "G", "start": 430 } ], "gene": "http://reg.genome.network/gene/GN006826", "geneNCBI_id": 4125, "geneSymbol": "MAN2B1", "hgvs": [ "ENST00000593686.1:c.431G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS394306" }, { "coordinates": [ { "allele": "A", "end": 435, "referenceAllele": "G", "start": 434 } ], "gene": "http://reg.genome.network/gene/GN006826", "geneNCBI_id": 4125, "geneSymbol": "MAN2B1", "hgvs": [ "ENST00000595880.5:n.435G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS395280" }, { "coordinates": [ { "allele": "A", "end": 194, "endIntronDirection": "-", "endIntronOffset": 23, "referenceAllele": "G", "start": 194, "startIntronDirection": "-", "startIntronOffset": 24 } ], "gene": "http://reg.genome.network/gene/GN006826", "geneNCBI_id": 4125, "geneSymbol": "MAN2B1", "hgvs": [ "ENST00000596591.1:c.195-24G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS395589" }, { "@id": "http://reg.genome.network/allele/PA658664280", "coordinates": [ { "allele": "A", "end": 1914, "referenceAllele": "G", "start": 1913 } ], "gene": "http://reg.genome.network/gene/GN006826", "geneNCBI_id": 4125, "geneSymbol": "MAN2B1", "hgvs": [ "NM_000528.3:c.1838G>A" ], "proteinEffect": { "hgvs": "NP_000519.2:p.Arg613Gln", "hgvsWellDefined": "NP_000519.2:p.Arg613Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS006585" }, { "@id": "http://reg.genome.network/allele/PA2826093405", "coordinates": [ { "allele": "A", "end": 1911, "referenceAllele": "G", "start": 1910 } ], "gene": "http://reg.genome.network/gene/GN006826", "geneNCBI_id": 4125, "geneSymbol": "MAN2B1", "hgvs": [ "NM_001173498.1:c.1835G>A" ], "proteinEffect": { "hgvs": "NP_001166969.1:p.Arg612Gln", "hgvsWellDefined": "NP_001166969.1:p.Arg612Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS015607" }, { "coordinates": [ { "allele": "A", "end": 1895, "referenceAllele": "G", "start": 1894 } ], "gene": "http://reg.genome.network/gene/GN006826", "geneNCBI_id": 4125, "geneSymbol": "MAN2B1", "hgvs": [ "XM_005259913.1:c.1841G>A" ], "proteinEffect": { "hgvs": "XP_005259970.1:p.Arg614Gln", "hgvsWellDefined": "XP_005259970.1:p.Arg614Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS062591" }, { "coordinates": [ { "allele": "A", "end": 896, "referenceAllele": "G", "start": 895 } ], "gene": "http://reg.genome.network/gene/GN006826", "geneNCBI_id": 4125, "geneSymbol": "MAN2B1", "hgvs": [ "XM_011528017.1:c.737G>A" ], "proteinEffect": { "hgvs": "XP_011526319.1:p.Arg246Gln", "hgvsWellDefined": "XP_011526319.1:p.Arg246Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS095096" }, { "coordinates": [ { "allele": "A", "end": 1882, "referenceAllele": "G", "start": 1881 } ], "gene": "http://reg.genome.network/gene/GN006826", "geneNCBI_id": 4125, "geneSymbol": "MAN2B1", "hgvs": [ "XM_005259913.2:c.1841G>A" ], "proteinEffect": { "hgvs": "XP_005259970.1:p.Arg614Gln", "hgvsWellDefined": "XP_005259970.1:p.Arg614Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS535086" }, { "coordinates": [ { "allele": "A", "end": 1780, "referenceAllele": "G", "start": 1779 } ], "gene": "http://reg.genome.network/gene/GN006826", "geneNCBI_id": 4125, "geneSymbol": "MAN2B1", "hgvs": [ "XM_024451518.1:c.737G>A" ], "proteinEffect": { "hgvs": "XP_024307286.1:p.Arg246Gln", "hgvsWellDefined": "XP_024307286.1:p.Arg246Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS585031" }, { "@id": "http://reg.genome.network/allele/PA658664280", "coordinates": [ { "allele": "A", "end": 1879, "referenceAllele": "G", "start": 1878 } ], "gene": "http://reg.genome.network/gene/GN006826", "geneNCBI_id": 4125, "geneSymbol": "MAN2B1", "hgvs": [ "NM_000528.4:c.1838G>A" ], "proteinEffect": { "hgvs": "NP_000519.2:p.Arg613Gln", "hgvsWellDefined": "NP_000519.2:p.Arg613Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS662473", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000456935.7:c.1838G>A" }, "RefSeq": { "hgvs": "NM_000528.4:c.1838G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000395473.2:p.Arg613Gln" }, "RefSeq": { "hgvs": "NP_000519.2:p.Arg613Gln" } } } }, { "@id": "http://reg.genome.network/allele/PA2826093405", "coordinates": [ { "allele": "A", "end": 1876, "referenceAllele": "G", "start": 1875 } ], "gene": "http://reg.genome.network/gene/GN006826", "geneNCBI_id": 4125, "geneSymbol": "MAN2B1", "hgvs": [ "NM_001173498.2:c.1835G>A" ], "proteinEffect": { "hgvs": "NP_001166969.1:p.Arg612Gln", "hgvsWellDefined": "NP_001166969.1:p.Arg612Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS713478" } ], "type": "nucleotide" }