{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA397079640", "communityStandardTitle": [ "NM_000512.5(GALNS):c.752G>A (p.Arg251Gln)" ], "externalRecords": { "COSMIC": [ { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=4848485", "active": true, "id": "COSM4848485" } ], "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=1036272[alleleid]", "alleleId": 1036272, "preferredName": "NM_000512.5(GALNS):c.752G>A (p.Arg251Gln)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/1048210", "RCV": [ "RCV001578313" ], "variationId": 1048210 } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr16:g.88902139C>T?assembly=hg19", "id": "chr16:g.88902139C>T" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr16:g.88835731C>T?assembly=hg38", "id": "chr16:g.88835731C>T" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/1199639828", "rs": 1199639828 } ], "gnomAD_3": [ { "@id": "http://gnomad.broadinstitute.org/variant/16-88835731-C-T?dataset=gnomad_r3", "id": "16-88835731-C-T", "variant": "16:88835731 C / T" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/16-88835731-C-T?dataset=gnomad_r4", "id": "16-88835731-C-T", "variant": "16:88835731 C / T" } ] }, "genomicAlleles": [ { "chromosome": "16", "coordinates": [ { "allele": "T", "end": 88835731, "referenceAllele": "C", "start": 88835730 } ], "hgvs": [ "NC_000016.10:g.88835731C>T", "CM000678.2:g.88835731C>T" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000064" }, { "chromosome": "16", "coordinates": [ { "allele": "T", "end": 88902139, "referenceAllele": "C", "start": 88902138 } ], "hgvs": [ "NC_000016.9:g.88902139C>T", "CM000678.1:g.88902139C>T" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000040" }, { "chromosome": "16", "coordinates": [ { "allele": "T", "end": 87429640, "referenceAllele": "C", "start": 87429639 } ], "hgvs": [ "NC_000016.8:g.87429640C>T" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000016" }, { "coordinates": [ { "allele": "A", "end": 26236, "referenceAllele": "G", "start": 26235 } ], "hgvs": [ "NG_008667.1:g.26236G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS001157" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 822, "referenceAllele": "G", "start": 821 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "ENST00000268695.10:c.752G>A" ], "proteinEffect": { "hgvs": "ENSP00000268695.5:p.Arg251Gln", "hgvsWellDefined": "ENSP00000268695.5:p.Arg251Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS743065", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000268695.10:c.752G>A" }, "RefSeq": { "hgvs": "NM_000512.5:c.752G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000268695.5:p.Arg251Gln" }, "RefSeq": { "hgvs": "NP_000503.1:p.Arg251Gln" } } } }, { "coordinates": [ { "allele": "A", "end": 841, "referenceAllele": "G", "start": 840 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "ENST00000268695.9:c.752G>A" ], "proteinEffect": { "hgvs": "ENSP00000268695.5:p.Arg251Gln", "hgvsWellDefined": "ENSP00000268695.5:p.Arg251Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS252095" }, { "coordinates": [ { "allele": "A", "end": 4161, "referenceAllele": "G", "start": 4160 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "ENST00000562593.5:n.4161G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS376891" }, { "coordinates": [ { "allele": "A", "end": 340, "referenceAllele": "G", "start": 339 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "ENST00000562931.5:n.340G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS377098" }, { "coordinates": [ { "allele": "A", "end": 454, "referenceAllele": "G", "start": 453 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "ENST00000566563.1:n.454G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS379525" }, { "coordinates": [ { "allele": "A", "end": 433, "referenceAllele": "G", "start": 432 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "ENST00000567525.5:c.433G>A" ], "proteinEffect": { "hgvs": "ENSP00000454484.1:n.433G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS380166" }, { "coordinates": [ { "allele": "A", "end": 871, "referenceAllele": "G", "start": 870 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "ENST00000568613.5:c.871G>A" ], "proteinEffect": { "hgvs": "ENSP00000457921.1:n.871G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS380908" }, { "@id": "http://reg.genome.network/allele/PA2825204581", "coordinates": [ { "allele": "A", "end": 841, "referenceAllele": "G", "start": 840 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "NM_000512.4:c.752G>A" ], "proteinEffect": { "hgvs": "NP_000503.1:p.Arg251Gln", "hgvsWellDefined": "NP_000503.1:p.Arg251Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS006568" }, { "coordinates": [ { "allele": "A", "end": 841, "referenceAllele": "G", "start": 840 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "XM_005256301.2:c.752G>A" ], "proteinEffect": { "hgvs": "XP_005256358.1:p.Arg251Gln", "hgvsWellDefined": "XP_005256358.1:p.Arg251Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS061259" }, { "coordinates": [ { "allele": "A", "end": 887, "referenceAllele": "G", "start": 886 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "XM_005256302.1:c.770G>A" ], "proteinEffect": { "hgvs": "XP_005256359.1:p.Arg257Gln", "hgvsWellDefined": "XP_005256359.1:p.Arg257Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS061260" }, { "coordinates": [ { "allele": "A", "end": 887, "referenceAllele": "G", "start": 886 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "XM_011522982.1:c.770G>A" ], "proteinEffect": { "hgvs": "XP_011521284.1:p.Arg257Gln", "hgvsWellDefined": "XP_011521284.1:p.Arg257Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS090123" }, { "coordinates": [ { "allele": "A", "end": 887, "referenceAllele": "G", "start": 886 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "XM_011522984.1:c.770G>A" ], "proteinEffect": { "hgvs": "XP_011521286.1:p.Arg257Gln", "hgvsWellDefined": "XP_011521286.1:p.Arg257Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS090124" }, { "@id": "http://reg.genome.network/allele/PA2499249015", "coordinates": [ { "allele": "A", "end": 721, "referenceAllele": "G", "start": 720 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "NM_001323543.1:c.197G>A" ], "proteinEffect": { "hgvs": "NP_001310472.1:p.Arg66Gln", "hgvsWellDefined": "NP_001310472.1:p.Arg66Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS515441" }, { "@id": "http://reg.genome.network/allele/PA2827194343", "coordinates": [ { "allele": "A", "end": 1015, "referenceAllele": "G", "start": 1014 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "NM_001323544.1:c.770G>A" ], "proteinEffect": { "hgvs": "NP_001310473.1:p.Arg257Gln", "hgvsWellDefined": "NP_001310473.1:p.Arg257Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS515442" }, { "coordinates": [ { "allele": "A", "end": 841, "referenceAllele": "G", "start": 840 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "XM_005256301.3:c.752G>A" ], "proteinEffect": { "hgvs": "XP_005256358.1:p.Arg251Gln", "hgvsWellDefined": "XP_005256358.1:p.Arg251Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS534454" }, { "coordinates": [ { "allele": "A", "end": 887, "referenceAllele": "G", "start": 886 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "XM_011522982.2:c.770G>A" ], "proteinEffect": { "hgvs": "XP_011521284.1:p.Arg257Gln", "hgvsWellDefined": "XP_011521284.1:p.Arg257Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS546838" }, { "coordinates": [ { "allele": "A", "end": 3172, "referenceAllele": "G", "start": 3171 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "XM_017023111.2:c.770G>A" ], "proteinEffect": { "hgvs": "XP_016878600.1:p.Arg257Gln", "hgvsWellDefined": "XP_016878600.1:p.Arg257Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS573926" }, { "coordinates": [ { "allele": "A", "end": 3172, "referenceAllele": "G", "start": 3171 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "XM_017023112.2:c.770G>A" ], "proteinEffect": { "hgvs": "XP_016878601.1:p.Arg257Gln", "hgvsWellDefined": "XP_016878601.1:p.Arg257Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS573927" }, { "coordinates": [ { "allele": "A", "end": 699, "referenceAllele": "G", "start": 698 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "XM_017023113.1:c.197G>A" ], "proteinEffect": { "hgvs": "XP_016878602.1:p.Arg66Gln", "hgvsWellDefined": "XP_016878602.1:p.Arg66Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS573928" }, { "@id": "http://reg.genome.network/allele/PA2825204581", "coordinates": [ { "allele": "A", "end": 822, "referenceAllele": "G", "start": 821 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "NM_000512.5:c.752G>A" ], "proteinEffect": { "hgvs": "NP_000503.1:p.Arg251Gln", "hgvsWellDefined": "NP_000503.1:p.Arg251Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS662466", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000268695.10:c.752G>A" }, "RefSeq": { "hgvs": "NM_000512.5:c.752G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000268695.5:p.Arg251Gln" }, "RefSeq": { "hgvs": "NP_000503.1:p.Arg251Gln" } } } }, { "@id": "http://reg.genome.network/allele/PA2499249015", "coordinates": [ { "allele": "A", "end": 698, "referenceAllele": "G", "start": 697 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "NM_001323543.2:c.197G>A" ], "proteinEffect": { "hgvs": "NP_001310472.1:p.Arg66Gln", "hgvsWellDefined": "NP_001310472.1:p.Arg66Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS686042" }, { "@id": "http://reg.genome.network/allele/PA2827194343", "coordinates": [ { "allele": "A", "end": 992, "referenceAllele": "G", "start": 991 } ], "gene": "http://reg.genome.network/gene/GN004122", "geneNCBI_id": 2588, "geneSymbol": "GALNS", "hgvs": [ "NM_001323544.2:c.770G>A" ], "proteinEffect": { "hgvs": "NP_001310473.1:p.Arg257Gln", "hgvsWellDefined": "NP_001310473.1:p.Arg257Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS686043" } ], "type": "nucleotide" }