{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA404317460", "communityStandardTitle": [ "NM_000159.4(GCDH):c.397G>A (p.Val133Met)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=468496[alleleid]", "alleleId": 468496, "preferredName": "NM_000159.4(GCDH):c.397G>A (p.Val133Met)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/459951", "RCV": [ "RCV000531618", "RCV004526700" ], "variationId": 459951 } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr19:g.13004359G>A?assembly=hg19", "id": "chr19:g.13004359G>A" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr19:g.12893545G>A?assembly=hg38", "id": "chr19:g.12893545G>A" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/746388510", "rs": 746388510 } ], "gnomAD_2": [ { "@id": "http://gnomad.broadinstitute.org/variant/19-13004359-G-A?dataset=gnomad_r2_1", "id": "19-13004359-G-A", "variant": "19:13004359 G / A" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/19-12893545-G-A?dataset=gnomad_r4", "id": "19-12893545-G-A", "variant": "19:12893545 G / A" } ] }, "genomicAlleles": [ { "chromosome": "19", "coordinates": [ { "allele": "A", "end": 12893545, "referenceAllele": "G", "start": 12893544 } ], "hgvs": [ "NC_000019.10:g.12893545G>A", "CM000681.2:g.12893545G>A" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000067" }, { "chromosome": "19", "coordinates": [ { "allele": "A", "end": 13004359, "referenceAllele": "G", "start": 13004358 } ], "hgvs": [ "NC_000019.9:g.13004359G>A", "CM000681.1:g.13004359G>A" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000043" }, { "chromosome": "19", "coordinates": [ { "allele": "A", "end": 12865359, "referenceAllele": "G", "start": 12865358 } ], "hgvs": [ "NC_000019.8:g.12865359G>A" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000019" }, { "coordinates": [ { "allele": "A", "end": 7386, "referenceAllele": "G", "start": 7385 } ], "hgvs": [ "NG_009292.1:g.7386G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS001548" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 474, "referenceAllele": "G", "start": 473 } ], "gene": "http://reg.genome.network/gene/GN004189", "geneNCBI_id": 2639, "geneSymbol": "GCDH", "hgvs": [ "ENST00000222214.10:c.397G>A" ], "proteinEffect": { "hgvs": "ENSP00000222214.4:p.Val133Met", "hgvsWellDefined": "ENSP00000222214.4:p.Val133Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS740551", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000222214.10:c.397G>A" }, "RefSeq": { "hgvs": "NM_000159.4:c.397G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000222214.4:p.Val133Met" }, "RefSeq": { "hgvs": "NP_000150.1:p.Val133Met" } } } }, { "coordinates": [ { "allele": "A", "end": 608, "referenceAllele": "G", "start": 607 } ], "gene": "http://reg.genome.network/gene/GN004189", "geneNCBI_id": 2639, "geneSymbol": "GCDH", "hgvs": [ "ENST00000222214.9:c.397G>A" ], "proteinEffect": { "hgvs": "ENSP00000222214.4:p.Val133Met", "hgvsWellDefined": "ENSP00000222214.4:p.Val133Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS248350" }, { "coordinates": [ { "allele": "A", "end": 375, "referenceAllele": "G", "start": 374 } ], "gene": "http://reg.genome.network/gene/GN004189", "geneNCBI_id": 2639, "geneSymbol": "GCDH", "hgvs": [ "ENST00000421816.6:n.375G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS286984" }, { "coordinates": [ { "allele": "A", "end": 762, "referenceAllele": "G", "start": 761 } ], "gene": "http://reg.genome.network/gene/GN004189", "geneNCBI_id": 2639, "geneSymbol": "GCDH", "hgvs": [ "ENST00000585420.5:n.762G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS388707" }, { "coordinates": [ { "allele": "A", "end": 454, "referenceAllele": "G", "start": 453 } ], "gene": "http://reg.genome.network/gene/GN004189", "geneNCBI_id": 2639, "geneSymbol": "GCDH", "hgvs": [ "ENST00000587832.5:n.454G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS390355" }, { "coordinates": [ { "allele": "A", "end": 430, "referenceAllele": "G", "start": 429 } ], "gene": "http://reg.genome.network/gene/GN004189", "geneNCBI_id": 2639, "geneSymbol": "GCDH", "hgvs": [ "ENST00000588905.5:c.361G>A" ], "proteinEffect": { "hgvs": "ENSP00000465770.1:p.Val121Met", "hgvsWellDefined": "ENSP00000465770.1:p.Val121Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS391110" }, { "coordinates": [ { "allele": "A", "end": 411, "referenceAllele": "G", "start": 410 } ], "gene": "http://reg.genome.network/gene/GN004189", "geneNCBI_id": 2639, "geneSymbol": "GCDH", "hgvs": [ "ENST00000589039.5:c.334G>A" ], "proteinEffect": { "hgvs": "ENSP00000465618.1:p.Val112Met", "hgvsWellDefined": "ENSP00000465618.1:p.Val112Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS391208" }, { "coordinates": [ { "allele": "A", "end": 523, "referenceAllele": "G", "start": 522 } ], "gene": "http://reg.genome.network/gene/GN004189", "geneNCBI_id": 2639, "geneSymbol": "GCDH", "hgvs": [ "ENST00000590530.5:c.452G>A" ], "proteinEffect": { "hgvs": "ENSP00000468452.1:p.Gly151Asp", "hgvsWellDefined": "ENSP00000468452.1:p.Gly151Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS392249" }, { "coordinates": [ { "allele": "A", "end": 762, "referenceAllele": "G", "start": 761 } ], "gene": "http://reg.genome.network/gene/GN004189", "geneNCBI_id": 2639, "geneSymbol": "GCDH", "hgvs": [ "ENST00000590627.5:n.762G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS392321" }, { "coordinates": [ { "allele": "A", "end": 433, "referenceAllele": "G", "start": 432 } ], "gene": "http://reg.genome.network/gene/GN004189", "geneNCBI_id": 2639, "geneSymbol": "GCDH", "hgvs": [ "ENST00000591043.1:n.433G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS392611" }, { "coordinates": [ { "allele": "A", "end": 542, "referenceAllele": "G", "start": 541 } ], "gene": "http://reg.genome.network/gene/GN004189", "geneNCBI_id": 2639, "geneSymbol": "GCDH", "hgvs": [ "ENST00000591470.5:c.397G>A" ], "proteinEffect": { "hgvs": "ENSP00000466845.1:p.Val133Met", "hgvsWellDefined": "ENSP00000466845.1:p.Val133Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS392892" }, { "@id": "http://reg.genome.network/allele/PA658676634", "coordinates": [ { "allele": "A", "end": 505, "referenceAllele": "G", "start": 504 } ], "gene": "http://reg.genome.network/gene/GN004189", "geneNCBI_id": 2639, "geneSymbol": "GCDH", "hgvs": [ "NM_000159.3:c.397G>A" ], "proteinEffect": { "hgvs": "NP_000150.1:p.Val133Met", "hgvsWellDefined": "NP_000150.1:p.Val133Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS006221" }, { "@id": "http://reg.genome.network/allele/PA916009026", "coordinates": [ { "allele": "A", "end": 505, "referenceAllele": "G", "start": 504 } ], "gene": "http://reg.genome.network/gene/GN004189", "geneNCBI_id": 2639, "geneSymbol": "GCDH", "hgvs": [ "NM_013976.3:c.397G>A" ], "proteinEffect": { "hgvs": "NP_039663.1:p.Val133Met", "hgvsWellDefined": "NP_039663.1:p.Val133Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS032843" }, { "coordinates": [ { "allele": "A", "end": 560, "referenceAllele": "G", "start": 559 } ], "gene": "http://reg.genome.network/gene/GN004189", "geneNCBI_id": 2639, "geneSymbol": "GCDH", "hgvs": [ "NR_102316.1:n.560G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS052774" }, { "coordinates": [ { "allele": "A", "end": 813, "referenceAllele": "G", "start": 812 } ], "gene": "http://reg.genome.network/gene/GN004189", "geneNCBI_id": 2639, "geneSymbol": "GCDH", "hgvs": [ "NR_102317.1:n.813G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS052775" }, { "coordinates": [ { "allele": "A", "end": 474, "referenceAllele": "G", "start": 473 } ], "gene": "http://reg.genome.network/gene/GN004189", "geneNCBI_id": 2639, "geneSymbol": "GCDH", "hgvs": [ "XM_006722721.2:c.397G>A" ], "proteinEffect": { "hgvs": "XP_006722784.1:p.Val133Met", "hgvsWellDefined": "XP_006722784.1:p.Val133Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS074704" }, { "coordinates": [ { "allele": "A", "end": 474, "referenceAllele": "G", "start": 473 } ], "gene": "http://reg.genome.network/gene/GN004189", "geneNCBI_id": 2639, "geneSymbol": "GCDH", "hgvs": [ "XM_011527899.1:c.397G>A" ], "proteinEffect": { "hgvs": "XP_011526201.1:p.Val133Met", "hgvsWellDefined": "XP_011526201.1:p.Val133Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS094980" }, { "coordinates": [ { "allele": "A", "end": 474, "referenceAllele": "G", "start": 473 } ], "gene": "http://reg.genome.network/gene/GN004189", "geneNCBI_id": 2639, "geneSymbol": "GCDH", "hgvs": [ "XM_011527900.1:c.397G>A" ], "proteinEffect": { "hgvs": "XP_011526202.1:p.Val133Met", "hgvsWellDefined": "XP_011526202.1:p.Val133Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS094981" }, { "coordinates": [ { "allele": "A", "end": 474, "referenceAllele": "G", "start": 473 } ], "gene": "http://reg.genome.network/gene/GN004189", "geneNCBI_id": 2639, "geneSymbol": "GCDH", "hgvs": [ "XM_011527899.2:c.397G>A" ], "proteinEffect": { "hgvs": "XP_011526201.1:p.Val133Met", "hgvsWellDefined": "XP_011526201.1:p.Val133Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS548874" }, { "coordinates": [ { "allele": "A", "end": 474, "referenceAllele": "G", "start": 473 } ], "gene": "http://reg.genome.network/gene/GN004189", "geneNCBI_id": 2639, "geneSymbol": "GCDH", "hgvs": [ "XM_011527900.2:c.397G>A" ], "proteinEffect": { "hgvs": "XP_011526202.1:p.Val133Met", "hgvsWellDefined": "XP_011526202.1:p.Val133Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS548875" }, { "coordinates": [ { "allele": "A", "end": 474, "referenceAllele": "G", "start": 473 } ], "gene": "http://reg.genome.network/gene/GN004189", "geneNCBI_id": 2639, "geneSymbol": "GCDH", "hgvs": [ "XM_017026580.1:c.397G>A" ], "proteinEffect": { "hgvs": "XP_016882069.1:p.Val133Met", "hgvsWellDefined": "XP_016882069.1:p.Val133Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS576706" }, { "@id": "http://reg.genome.network/allele/PA658676634", "coordinates": [ { "allele": "A", "end": 474, "referenceAllele": "G", "start": 473 } ], "gene": "http://reg.genome.network/gene/GN004189", "geneNCBI_id": 2639, "geneSymbol": "GCDH", "hgvs": [ "NM_000159.4:c.397G>A" ], "proteinEffect": { "hgvs": "NP_000150.1:p.Val133Met", "hgvsWellDefined": "NP_000150.1:p.Val133Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS662332", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000222214.10:c.397G>A" }, "RefSeq": { "hgvs": "NM_000159.4:c.397G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000222214.4:p.Val133Met" }, "RefSeq": { "hgvs": "NP_000150.1:p.Val133Met" } } } }, { "@id": "http://reg.genome.network/allele/PA916009026", "coordinates": [ { "allele": "A", "end": 474, "referenceAllele": "G", "start": 473 } ], "gene": "http://reg.genome.network/gene/GN004189", "geneNCBI_id": 2639, "geneSymbol": "GCDH", "hgvs": [ "NM_013976.4:c.397G>A" ], "proteinEffect": { "hgvs": "NP_039663.1:p.Val133Met", "hgvsWellDefined": "NP_039663.1:p.Val133Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS697153" }, { "@id": "http://reg.genome.network/allele/PA916009026", "coordinates": [ { "allele": "A", "end": 474, "referenceAllele": "G", "start": 473 } ], "gene": "http://reg.genome.network/gene/GN004189", "geneNCBI_id": 2639, "geneSymbol": "GCDH", "hgvs": [ "NM_013976.5:c.397G>A" ], "proteinEffect": { "hgvs": "NP_039663.1:p.Val133Met", "hgvsWellDefined": "NP_039663.1:p.Val133Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS727927" } ], "type": "nucleotide" }