{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA118908", "communityStandardTitle": [ "NM_006214.4(PHYH):c.824G>A (p.Arg275Gln)" ], "externalRecords": { "COSMIC": [ { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=4714200", "active": true, "id": "COSM4714200" } ], "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=22627[alleleid]", "alleleId": 22627, "preferredName": "NM_006214.4(PHYH):c.824G>A (p.Arg275Gln)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/7588", "RCV": [ "RCV000008026", "RCV001851728", "RCV003473056" ], "variationId": 7588 } ], "ExAC": [ { "@id": "http://exac.broadinstitute.org/variant/10-13325694-C-T", "id": "10-13325694-C-T", "variant": "10:13325694 C / T" } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr10:g.13325694C>T?assembly=hg19", "id": "chr10:g.13325694C>T" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr10:g.13283694C>T?assembly=hg38", "id": "chr10:g.13283694C>T" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/104894174", "rs": 104894174 } ], "gnomAD_2": [ { "@id": "http://gnomad.broadinstitute.org/variant/10-13325694-C-T?dataset=gnomad_r2_1", "id": "10-13325694-C-T", "variant": "10:13325694 C / T" } ], "gnomAD_3": [ { "@id": "http://gnomad.broadinstitute.org/variant/10-13283694-C-T?dataset=gnomad_r3", "id": "10-13283694-C-T", "variant": "10:13283694 C / T" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/10-13283694-C-T?dataset=gnomad_r4", "id": "10-13283694-C-T", "variant": "10:13283694 C / T" } ] }, "genomicAlleles": [ { "chromosome": "10", "coordinates": [ { "allele": "T", "end": 13283694, "referenceAllele": "C", "start": 13283693 } ], "hgvs": [ "NC_000010.11:g.13283694C>T", "CM000672.2:g.13283694C>T" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000058" }, { "chromosome": "10", "coordinates": [ { "allele": "T", "end": 13325694, "referenceAllele": "C", "start": 13325693 } ], "hgvs": [ "NC_000010.10:g.13325694C>T", "CM000672.1:g.13325694C>T" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000034" }, { "chromosome": "10", "coordinates": [ { "allele": "T", "end": 13365700, "referenceAllele": "C", "start": 13365699 } ], "hgvs": [ "NC_000010.9:g.13365700C>T" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000010" }, { "coordinates": [ { "allele": "A", "end": 21437, "referenceAllele": "G", "start": 21436 } ], "hgvs": [ "NG_012862.1:g.21437G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS002591" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 846, "referenceAllele": "G", "start": 845 } ], "gene": "http://reg.genome.network/gene/GN008940", "geneNCBI_id": 5264, "geneSymbol": "PHYH", "hgvs": [ "ENST00000263038.9:c.824G>A" ], "proteinEffect": { "hgvs": "ENSP00000263038.4:p.Arg275Gln", "hgvsWellDefined": "ENSP00000263038.4:p.Arg275Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS742438", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000263038.9:c.824G>A" }, "RefSeq": { "hgvs": "NM_006214.4:c.824G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000263038.4:p.Arg275Gln" }, "RefSeq": { "hgvs": "NP_006205.1:p.Arg275Gln" } } } }, { "coordinates": [ { "allele": "A", "end": 883, "referenceAllele": "G", "start": 882 } ], "gene": "http://reg.genome.network/gene/GN008940", "geneNCBI_id": 5264, "geneSymbol": "PHYH", "hgvs": [ "ENST00000263038.8:c.824G>A" ], "proteinEffect": { "hgvs": "ENSP00000263038.4:p.Arg275Gln", "hgvsWellDefined": "ENSP00000263038.4:p.Arg275Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS251170" }, { "coordinates": [ { "allele": "A", "end": 1034, "referenceAllele": "G", "start": 1033 } ], "gene": "http://reg.genome.network/gene/GN008940", "geneNCBI_id": 5264, "geneSymbol": "PHYH", "hgvs": [ "ENST00000396913.6:c.524G>A" ], "proteinEffect": { "hgvs": "ENSP00000380121.2:p.Arg175Gln", "hgvsWellDefined": "ENSP00000380121.2:p.Arg175Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS277500" }, { "coordinates": [ { "allele": "A", "end": 1178, "referenceAllele": "G", "start": 1177 } ], "gene": "http://reg.genome.network/gene/GN008940", "geneNCBI_id": 5264, "geneSymbol": "PHYH", "hgvs": [ "ENST00000396920.7:c.773G>A" ], "proteinEffect": { "hgvs": "ENSP00000380126.3:p.Arg258Gln", "hgvsWellDefined": "ENSP00000380126.3:p.Arg258Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS277502" }, { "coordinates": [ { "allele": "A", "end": 879, "referenceAllele": "G", "start": 878 } ], "gene": "http://reg.genome.network/gene/GN008940", "geneNCBI_id": 5264, "geneSymbol": "PHYH", "hgvs": [ "ENST00000453759.6:c.524G>A" ], "proteinEffect": { "hgvs": "ENSP00000412525.2:p.Arg175Gln", "hgvsWellDefined": "ENSP00000412525.2:p.Arg175Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS302261" }, { "@id": "http://reg.genome.network/allele/PA2825380852", "coordinates": [ { "allele": "A", "end": 1017, "referenceAllele": "G", "start": 1016 } ], "gene": "http://reg.genome.network/gene/GN008940", "geneNCBI_id": 5264, "geneSymbol": "PHYH", "hgvs": [ "NM_001037537.1:c.524G>A" ], "proteinEffect": { "hgvs": "NP_001032626.1:p.Arg175Gln", "hgvsWellDefined": "NP_001032626.1:p.Arg175Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS009280" }, { "@id": "http://reg.genome.network/allele/PA108232", "coordinates": [ { "allele": "A", "end": 912, "referenceAllele": "G", "start": 911 } ], "gene": "http://reg.genome.network/gene/GN008940", "geneNCBI_id": 5264, "geneSymbol": "PHYH", "hgvs": [ "NM_006214.3:c.824G>A" ], "proteinEffect": { "hgvs": "NP_006205.1:p.Arg275Gln", "hgvsWellDefined": "NP_006205.1:p.Arg275Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS031238" }, { "coordinates": [ { "allele": "A", "end": 656, "referenceAllele": "G", "start": 655 } ], "gene": "http://reg.genome.network/gene/GN008940", "geneNCBI_id": 5264, "geneSymbol": "PHYH", "hgvs": [ "XM_005252469.2:c.605G>A" ], "proteinEffect": { "hgvs": "XP_005252526.1:p.Arg202Gln", "hgvsWellDefined": "XP_005252526.1:p.Arg202Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS059956" }, { "@id": "http://reg.genome.network/allele/PA2827185512", "coordinates": [ { "allele": "A", "end": 1076, "referenceAllele": "G", "start": 1075 } ], "gene": "http://reg.genome.network/gene/GN008940", "geneNCBI_id": 5264, "geneSymbol": "PHYH", "hgvs": [ "NM_001323080.1:c.524G>A" ], "proteinEffect": { "hgvs": "NP_001310009.1:p.Arg175Gln", "hgvsWellDefined": "NP_001310009.1:p.Arg175Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS515278" }, { "@id": "http://reg.genome.network/allele/PA916026799", "coordinates": [ { "allele": "A", "end": 918, "referenceAllele": "G", "start": 917 } ], "gene": "http://reg.genome.network/gene/GN008940", "geneNCBI_id": 5264, "geneSymbol": "PHYH", "hgvs": [ "NM_001323082.1:c.830G>A" ], "proteinEffect": { "hgvs": "NP_001310011.1:p.Arg277Gln", "hgvsWellDefined": "NP_001310011.1:p.Arg277Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS515279" }, { "@id": "http://reg.genome.network/allele/PA2827185908", "coordinates": [ { "allele": "A", "end": 648, "referenceAllele": "G", "start": 647 } ], "gene": "http://reg.genome.network/gene/GN008940", "geneNCBI_id": 5264, "geneSymbol": "PHYH", "hgvs": [ "NM_001323083.1:c.560G>A" ], "proteinEffect": { "hgvs": "NP_001310012.1:p.Arg187Gln", "hgvsWellDefined": "NP_001310012.1:p.Arg187Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS515280" }, { "@id": "http://reg.genome.network/allele/PA2827186067", "coordinates": [ { "allele": "A", "end": 1023, "referenceAllele": "G", "start": 1022 } ], "gene": "http://reg.genome.network/gene/GN008940", "geneNCBI_id": 5264, "geneSymbol": "PHYH", "hgvs": [ "NM_001323084.1:c.530G>A" ], "proteinEffect": { "hgvs": "NP_001310013.1:p.Arg177Gln", "hgvsWellDefined": "NP_001310013.1:p.Arg177Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS515281" }, { "@id": "http://reg.genome.network/allele/PA108232", "coordinates": [ { "allele": "A", "end": 846, "referenceAllele": "G", "start": 845 } ], "gene": "http://reg.genome.network/gene/GN008940", "geneNCBI_id": 5264, "geneSymbol": "PHYH", "hgvs": [ "NM_006214.4:c.824G>A" ], "proteinEffect": { "hgvs": "NP_006205.1:p.Arg275Gln", "hgvsWellDefined": "NP_006205.1:p.Arg275Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS667340", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000263038.9:c.824G>A" }, "RefSeq": { "hgvs": "NM_006214.4:c.824G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000263038.4:p.Arg275Gln" }, "RefSeq": { "hgvs": "NP_006205.1:p.Arg275Gln" } } } }, { "@id": "http://reg.genome.network/allele/PA2825380852", "coordinates": [ { "allele": "A", "end": 1034, "referenceAllele": "G", "start": 1033 } ], "gene": "http://reg.genome.network/gene/GN008940", "geneNCBI_id": 5264, "geneSymbol": "PHYH", "hgvs": [ "NM_001037537.2:c.524G>A" ], "proteinEffect": { "hgvs": "NP_001032626.1:p.Arg175Gln", "hgvsWellDefined": "NP_001032626.1:p.Arg175Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS711576" }, { "@id": "http://reg.genome.network/allele/PA2827185512", "coordinates": [ { "allele": "A", "end": 1093, "referenceAllele": "G", "start": 1092 } ], "gene": "http://reg.genome.network/gene/GN008940", "geneNCBI_id": 5264, "geneSymbol": "PHYH", "hgvs": [ "NM_001323080.2:c.524G>A" ], "proteinEffect": { "hgvs": "NP_001310009.1:p.Arg175Gln", "hgvsWellDefined": "NP_001310009.1:p.Arg175Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS718298" }, { "@id": "http://reg.genome.network/allele/PA916026799", "coordinates": [ { "allele": "A", "end": 852, "referenceAllele": "G", "start": 851 } ], "gene": "http://reg.genome.network/gene/GN008940", "geneNCBI_id": 5264, "geneSymbol": "PHYH", "hgvs": [ "NM_001323082.2:c.830G>A" ], "proteinEffect": { "hgvs": "NP_001310011.1:p.Arg277Gln", "hgvsWellDefined": "NP_001310011.1:p.Arg277Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS718299" }, { "@id": "http://reg.genome.network/allele/PA2827185908", "coordinates": [ { "allele": "A", "end": 582, "referenceAllele": "G", "start": 581 } ], "gene": "http://reg.genome.network/gene/GN008940", "geneNCBI_id": 5264, "geneSymbol": "PHYH", "hgvs": [ "NM_001323083.2:c.560G>A" ], "proteinEffect": { "hgvs": "NP_001310012.1:p.Arg187Gln", "hgvsWellDefined": "NP_001310012.1:p.Arg187Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS718300" }, { "@id": "http://reg.genome.network/allele/PA2827186067", "coordinates": [ { "allele": "A", "end": 1040, "referenceAllele": "G", "start": 1039 } ], "gene": "http://reg.genome.network/gene/GN008940", "geneNCBI_id": 5264, "geneSymbol": "PHYH", "hgvs": [ "NM_001323084.2:c.530G>A" ], "proteinEffect": { "hgvs": "NP_001310013.1:p.Arg177Gln", "hgvsWellDefined": "NP_001310013.1:p.Arg177Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS718301" } ], "type": "nucleotide" }