{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA8235123", "communityStandardTitle": [ "NM_000512.5(GALNS):c.494G>A (p.Cys165Tyr)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=1036325[alleleid]", "alleleId": 1036325, "preferredName": "NM_000512.5(GALNS):c.494G>A (p.Cys165Tyr)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/1048196", "RCV": [ "RCV001578298" ], "variationId": 1048196 } ], "ExAC": [ { "@id": "http://exac.broadinstitute.org/variant/16-88904102-C-T", "id": "16-88904102-C-T", "variant": "16:88904102 C / T" } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr16:g.88904102C>T?assembly=hg19", "id": "chr16:g.88904102C>T" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr16:g.88837694C>T?assembly=hg38", "id": "chr16:g.88837694C>T" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/768757999", "rs": 768757999 } ], "gnomAD_2": [ { "@id": "http://gnomad.broadinstitute.org/variant/16-88904102-C-T?dataset=gnomad_r2_1", "id": "16-88904102-C-T", "variant": "16:88904102 C / T" } ] }, "genomicAlleles": [ { "chromosome": "16", "coordinates": [ { "allele": "T", "end": 88837694, "referenceAllele": "C", "start": 88837693 } ], "hgvs": [ "NC_000016.10:g.88837694C>T", "CM000678.2:g.88837694C>T" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000064" }, { "chromosome": "16", "coordinates": [ { "allele": "T", "end": 88904102, "referenceAllele": "C", "start": 88904101 } ], "hgvs": [ "NC_000016.9:g.88904102C>T", "CM000678.1:g.88904102C>T" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000040" }, { "chromosome": "16", "coordinates": [ { "allele": "T", "end": 87431603, "referenceAllele": "C", "start": 87431602 } ], "hgvs": [ "NC_000016.8:g.87431603C>T" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000016" }, { "coordinates": [ { "allele": "A", "end": 24273, "referenceAllele": "G", "start": 24272 } ], "hgvs": [ "NG_008667.1:g.24273G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS001157" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 564, "referenceAllele": "G", "start": 563 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "ENST00000268695.10:c.494G>A" ], "proteinEffect": { "hgvs": "ENSP00000268695.5:p.Cys165Tyr", "hgvsWellDefined": "ENSP00000268695.5:p.Cys165Tyr" }, "referenceSequence": "http://reg.genome.network/refseq/RS743065", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000268695.10:c.494G>A" }, "RefSeq": { "hgvs": "NM_000512.5:c.494G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000268695.5:p.Cys165Tyr" }, "RefSeq": { "hgvs": "NP_000503.1:p.Cys165Tyr" } } } }, { "coordinates": [ { "allele": "A", "end": 583, "referenceAllele": "G", "start": 582 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "ENST00000268695.9:c.494G>A" ], "proteinEffect": { "hgvs": "ENSP00000268695.5:p.Cys165Tyr", "hgvsWellDefined": "ENSP00000268695.5:p.Cys165Tyr" }, "referenceSequence": "http://reg.genome.network/refseq/RS252095" }, { "coordinates": [ { "allele": "A", "end": 450, "referenceAllele": "G", "start": 449 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "ENST00000561812.1:n.450G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS376369" }, { "coordinates": [ { "allele": "A", "end": 3903, "referenceAllele": "G", "start": 3902 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "ENST00000562593.5:n.3903G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS376891" }, { "coordinates": [ { "allele": "A", "end": 375, "referenceAllele": "G", "start": 374 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "ENST00000562831.1:c.278G>A" ], "proteinEffect": { "hgvs": "ENSP00000455174.1:p.Cys93Tyr", "hgvsWellDefined": "ENSP00000455174.1:p.Cys93Tyr" }, "referenceSequence": "http://reg.genome.network/refseq/RS377035" }, { "coordinates": [ { "allele": "A", "end": 82, "referenceAllele": "G", "start": 81 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "ENST00000562931.5:n.82G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS377098" }, { "coordinates": [ { "allele": "A", "end": 196, "referenceAllele": "G", "start": 195 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "ENST00000566563.1:n.196G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS379525" }, { "coordinates": [ { "allele": "A", "end": 247, "endIntronDirection": "-", "endIntronOffset": 1426, "referenceAllele": "G", "start": 247, "startIntronDirection": "-", "startIntronOffset": 1427 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "ENST00000567525.5:c.248-1427G>A" ], "proteinEffect": { "hgvs": "ENSP00000454484.1:n.248-1427G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS380166" }, { "coordinates": [ { "allele": "A", "end": 613, "referenceAllele": "G", "start": 612 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "ENST00000568613.5:c.613G>A" ], "proteinEffect": { "hgvs": "ENSP00000457921.1:n.613G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS380908" }, { "@id": "http://reg.genome.network/allele/PA2825204451", "coordinates": [ { "allele": "A", "end": 583, "referenceAllele": "G", "start": 582 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "NM_000512.4:c.494G>A" ], "proteinEffect": { "hgvs": "NP_000503.1:p.Cys165Tyr", "hgvsWellDefined": "NP_000503.1:p.Cys165Tyr" }, "referenceSequence": "http://reg.genome.network/refseq/RS006568" }, { "coordinates": [ { "allele": "A", "end": 583, "referenceAllele": "G", "start": 582 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "XM_005256301.2:c.494G>A" ], "proteinEffect": { "hgvs": "XP_005256358.1:p.Cys165Tyr", "hgvsWellDefined": "XP_005256358.1:p.Cys165Tyr" }, "referenceSequence": "http://reg.genome.network/refseq/RS061259" }, { "coordinates": [ { "allele": "A", "end": 629, "referenceAllele": "G", "start": 628 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "XM_005256302.1:c.512G>A" ], "proteinEffect": { "hgvs": "XP_005256359.1:p.Cys171Tyr", "hgvsWellDefined": "XP_005256359.1:p.Cys171Tyr" }, "referenceSequence": "http://reg.genome.network/refseq/RS061260" }, { "coordinates": [ { "allele": "A", "end": 629, "referenceAllele": "G", "start": 628 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "XM_011522982.1:c.512G>A" ], "proteinEffect": { "hgvs": "XP_011521284.1:p.Cys171Tyr", "hgvsWellDefined": "XP_011521284.1:p.Cys171Tyr" }, "referenceSequence": "http://reg.genome.network/refseq/RS090123" }, { "coordinates": [ { "allele": "A", "end": 629, "referenceAllele": "G", "start": 628 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "XM_011522984.1:c.512G>A" ], "proteinEffect": { "hgvs": "XP_011521286.1:p.Cys171Tyr", "hgvsWellDefined": "XP_011521286.1:p.Cys171Tyr" }, "referenceSequence": "http://reg.genome.network/refseq/RS090124" }, { "coordinates": [ { "allele": "A", "end": 463, "referenceAllele": "G", "start": 462 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "NM_001323543.1:c.-62G>A" ], "proteinEffect": { "hgvs": "NP_001310472.1:n.-62G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS515441" }, { "@id": "http://reg.genome.network/allele/PA2499249102", "coordinates": [ { "allele": "A", "end": 757, "referenceAllele": "G", "start": 756 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "NM_001323544.1:c.512G>A" ], "proteinEffect": { "hgvs": "NP_001310473.1:p.Cys171Tyr", "hgvsWellDefined": "NP_001310473.1:p.Cys171Tyr" }, "referenceSequence": "http://reg.genome.network/refseq/RS515442" }, { "coordinates": [ { "allele": "A", "end": 583, "referenceAllele": "G", "start": 582 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "XM_005256301.3:c.494G>A" ], "proteinEffect": { "hgvs": "XP_005256358.1:p.Cys165Tyr", "hgvsWellDefined": "XP_005256358.1:p.Cys165Tyr" }, "referenceSequence": "http://reg.genome.network/refseq/RS534454" }, { "coordinates": [ { "allele": "A", "end": 629, "referenceAllele": "G", "start": 628 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "XM_011522982.2:c.512G>A" ], "proteinEffect": { "hgvs": "XP_011521284.1:p.Cys171Tyr", "hgvsWellDefined": "XP_011521284.1:p.Cys171Tyr" }, "referenceSequence": "http://reg.genome.network/refseq/RS546838" }, { "coordinates": [ { "allele": "A", "end": 2914, "referenceAllele": "G", "start": 2913 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "XM_017023111.2:c.512G>A" ], "proteinEffect": { "hgvs": "XP_016878600.1:p.Cys171Tyr", "hgvsWellDefined": "XP_016878600.1:p.Cys171Tyr" }, "referenceSequence": "http://reg.genome.network/refseq/RS573926" }, { "coordinates": [ { "allele": "A", "end": 2914, "referenceAllele": "G", "start": 2913 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "XM_017023112.2:c.512G>A" ], "proteinEffect": { "hgvs": "XP_016878601.1:p.Cys171Tyr", "hgvsWellDefined": "XP_016878601.1:p.Cys171Tyr" }, "referenceSequence": "http://reg.genome.network/refseq/RS573927" }, { "coordinates": [ { "allele": "A", "end": 441, "referenceAllele": "G", "start": 440 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "XM_017023113.1:c.-62G>A" ], "proteinEffect": { "hgvs": "XP_016878602.1:n.-62G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS573928" }, { "@id": "http://reg.genome.network/allele/PA2825204451", "coordinates": [ { "allele": "A", "end": 564, "referenceAllele": "G", "start": 563 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "NM_000512.5:c.494G>A" ], "proteinEffect": { "hgvs": "NP_000503.1:p.Cys165Tyr", "hgvsWellDefined": "NP_000503.1:p.Cys165Tyr" }, "referenceSequence": "http://reg.genome.network/refseq/RS662466", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000268695.10:c.494G>A" }, "RefSeq": { "hgvs": "NM_000512.5:c.494G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000268695.5:p.Cys165Tyr" }, "RefSeq": { "hgvs": "NP_000503.1:p.Cys165Tyr" } } } }, { "coordinates": [ { "allele": "A", "end": 440, "referenceAllele": "G", "start": 439 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "NM_001323543.2:c.-62G>A" ], "proteinEffect": { "hgvs": "NP_001310472.1:n.-62G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS686042" }, { "@id": "http://reg.genome.network/allele/PA2499249102", "coordinates": [ { "allele": "A", "end": 734, "referenceAllele": "G", "start": 733 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "NM_001323544.2:c.512G>A" ], "proteinEffect": { "hgvs": "NP_001310473.1:p.Cys171Tyr", "hgvsWellDefined": "NP_001310473.1:p.Cys171Tyr" }, "referenceSequence": "http://reg.genome.network/refseq/RS686043" } ], "type": "nucleotide" }