{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA2451189", "communityStandardTitle": [ "NM_052859.4(RFT1):c.1271G>A (p.Arg424His)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=2120615[alleleid]", "alleleId": 2120615, "preferredName": "NM_052859.4(RFT1):c.1271G>A (p.Arg424His)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/2073967", "RCV": [ "RCV002975959", "RCV002975960" ], "variationId": 2073967 } ], "ExAC": [ { "@id": "http://exac.broadinstitute.org/variant/3-53126572-C-T", "id": "3-53126572-C-T", "variant": "3:53126572 C / T" } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr3:g.53126572C>T?assembly=hg19", "id": "chr3:g.53126572C>T" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr3:g.53092556C>T?assembly=hg38", "id": "chr3:g.53092556C>T" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/759492237", "rs": 759492237 } ], "gnomAD_2": [ { "@id": "http://gnomad.broadinstitute.org/variant/3-53126572-C-T?dataset=gnomad_r2_1", "id": "3-53126572-C-T", "variant": "3:53126572 C / T" } ], "gnomAD_3": [ { "@id": "http://gnomad.broadinstitute.org/variant/3-53092556-C-T?dataset=gnomad_r3", "id": "3-53092556-C-T", "variant": "3:53092556 C / T" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/3-53092556-C-T?dataset=gnomad_r4", "id": "3-53092556-C-T", "variant": "3:53092556 C / T" } ] }, "genomicAlleles": [ { "chromosome": "3", "coordinates": [ { "allele": "T", "end": 53092556, "referenceAllele": "C", "start": 53092555 } ], "hgvs": [ "NC_000003.12:g.53092556C>T", "CM000665.2:g.53092556C>T" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000051" }, { "chromosome": "3", "coordinates": [ { "allele": "T", "end": 53126572, "referenceAllele": "C", "start": 53126571 } ], "hgvs": [ "NC_000003.11:g.53126572C>T", "CM000665.1:g.53126572C>T" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000027" }, { "chromosome": "3", "coordinates": [ { "allele": "T", "end": 53101612, "referenceAllele": "C", "start": 53101611 } ], "hgvs": [ "NC_000003.10:g.53101612C>T" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000003" }, { "coordinates": [ { "allele": "A", "end": 42899, "referenceAllele": "G", "start": 42898 } ], "hgvs": [ "NG_009203.1:g.42899G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS001476" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 1306, "referenceAllele": "G", "start": 1305 } ], "gene": "http://reg.genome.network/gene/GN030220", "geneNCBI_id": 91869, "geneSymbol": "RFT1", "hgvs": [ "ENST00000296292.8:c.1271G>A" ], "proteinEffect": { "hgvs": "ENSP00000296292.3:p.Arg424His", "hgvsWellDefined": "ENSP00000296292.3:p.Arg424His" }, "referenceSequence": "http://reg.genome.network/refseq/RS744396", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000296292.8:c.1271G>A" }, "RefSeq": { "hgvs": "NM_052859.4:c.1271G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000296292.3:p.Arg424His" }, "RefSeq": { "hgvs": "NP_443091.1:p.Arg424His" } } } }, { "coordinates": [ { "allele": "A", "end": 1333, "referenceAllele": "G", "start": 1332 } ], "gene": "http://reg.genome.network/gene/GN030220", "geneNCBI_id": 91869, "geneSymbol": "RFT1", "hgvs": [ "ENST00000296292.7:c.1271G>A" ], "proteinEffect": { "hgvs": "ENSP00000296292.3:p.Arg424His", "hgvsWellDefined": "ENSP00000296292.3:p.Arg424His" }, "referenceSequence": "http://reg.genome.network/refseq/RS254271" }, { "coordinates": [ { "allele": "A", "end": 1207, "referenceAllele": "G", "start": 1206 } ], "gene": "http://reg.genome.network/gene/GN030220", "geneNCBI_id": 91869, "geneSymbol": "RFT1", "hgvs": [ "ENST00000394738.7:c.1154G>A" ], "proteinEffect": { "hgvs": "ENSP00000378223.3:p.Arg385His", "hgvsWellDefined": "ENSP00000378223.3:p.Arg385His" }, "referenceSequence": "http://reg.genome.network/refseq/RS276319" }, { "coordinates": [ { "allele": "A", "end": 73, "endIntronDirection": "-", "endIntronOffset": 6703, "referenceAllele": "G", "start": 73, "startIntronDirection": "-", "startIntronOffset": 6704 } ], "hgvs": [ "ENST00000607203.1:c.74-6704G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS399850" }, { "coordinates": [ { "allele": "A", "end": 136, "referenceAllele": "G", "start": 135 } ], "hgvs": [ "ENST00000607283.5:c.136G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS399863" }, { "coordinates": [ { "allele": "A", "end": 73, "endIntronDirection": "+", "endIntronOffset": 6825, "referenceAllele": "G", "start": 73, "startIntronDirection": "+", "startIntronOffset": 6824 } ], "hgvs": [ "ENST00000607495.5:c.73+6825G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS399899" }, { "@id": "http://reg.genome.network/allele/PA2580493885", "coordinates": [ { "allele": "A", "end": 1325, "referenceAllele": "G", "start": 1324 } ], "gene": "http://reg.genome.network/gene/GN030220", "geneNCBI_id": 91869, "geneSymbol": "RFT1", "hgvs": [ "NM_052859.3:c.1271G>A" ], "proteinEffect": { "hgvs": "NP_443091.1:p.Arg424His", "hgvsWellDefined": "NP_443091.1:p.Arg424His" }, "referenceSequence": "http://reg.genome.network/refseq/RS039857" }, { "coordinates": [ { "allele": "A", "end": 1267, "endIntronDirection": "-", "endIntronOffset": 6703, "referenceAllele": "G", "start": 1267, "startIntronDirection": "-", "startIntronOffset": 6704 } ], "gene": "http://reg.genome.network/gene/GN030220", "geneNCBI_id": 91869, "geneSymbol": "RFT1", "hgvs": [ "XM_006713384.2:c.1209-6704G>A" ], "proteinEffect": { "hgvs": "XP_006713447.1:n.1209-6704G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS070124" }, { "coordinates": [ { "allele": "A", "end": 1267, "endIntronDirection": "+", "endIntronOffset": 6825, "referenceAllele": "G", "start": 1267, "startIntronDirection": "+", "startIntronOffset": 6824 } ], "gene": "http://reg.genome.network/gene/GN030220", "geneNCBI_id": 91869, "geneSymbol": "RFT1", "hgvs": [ "XM_011534214.1:c.1208+6825G>A" ], "proteinEffect": { "hgvs": "XP_011532516.1:n.1208+6825G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS101232" }, { "coordinates": [ { "allele": "A", "end": 1267, "endIntronDirection": "+", "endIntronOffset": 6825, "referenceAllele": "G", "start": 1267, "startIntronDirection": "+", "startIntronOffset": 6824 } ], "gene": "http://reg.genome.network/gene/GN030220", "geneNCBI_id": 91869, "geneSymbol": "RFT1", "hgvs": [ "XM_011534215.1:c.1208+6825G>A" ], "proteinEffect": { "hgvs": "XP_011532517.1:n.1208+6825G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS101233" }, { "coordinates": [ { "allele": "A", "end": 844, "referenceAllele": "G", "start": 843 } ], "gene": "http://reg.genome.network/gene/GN030220", "geneNCBI_id": 91869, "geneSymbol": "RFT1", "hgvs": [ "XM_011534216.1:c.614G>A" ], "proteinEffect": { "hgvs": "XP_011532518.1:p.Arg205His", "hgvsWellDefined": "XP_011532518.1:p.Arg205His" }, "referenceSequence": "http://reg.genome.network/refseq/RS101234" }, { "coordinates": [ { "allele": "A", "end": 1267, "endIntronDirection": "-", "endIntronOffset": 6703, "referenceAllele": "G", "start": 1267, "startIntronDirection": "-", "startIntronOffset": 6704 } ], "gene": "http://reg.genome.network/gene/GN030220", "geneNCBI_id": 91869, "geneSymbol": "RFT1", "hgvs": [ "XR_940507.1:n.1268-6704G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS135203" }, { "coordinates": [ { "allele": "A", "end": 1273, "endIntronDirection": "-", "endIntronOffset": 6703, "referenceAllele": "G", "start": 1273, "startIntronDirection": "-", "startIntronOffset": 6704 } ], "gene": "http://reg.genome.network/gene/GN030220", "geneNCBI_id": 91869, "geneSymbol": "RFT1", "hgvs": [ "XM_006713384.3:c.1209-6704G>A" ], "proteinEffect": { "hgvs": "XP_006713447.1:n.1209-6704G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS538487" }, { "coordinates": [ { "allele": "A", "end": 1277, "endIntronDirection": "+", "endIntronOffset": 6825, "referenceAllele": "G", "start": 1277, "startIntronDirection": "+", "startIntronOffset": 6824 } ], "gene": "http://reg.genome.network/gene/GN030220", "geneNCBI_id": 91869, "geneSymbol": "RFT1", "hgvs": [ "XM_011534214.2:c.1208+6825G>A" ], "proteinEffect": { "hgvs": "XP_011532516.1:n.1208+6825G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS551566" }, { "coordinates": [ { "allele": "A", "end": 1276, "endIntronDirection": "+", "endIntronOffset": 6825, "referenceAllele": "G", "start": 1276, "startIntronDirection": "+", "startIntronOffset": 6824 } ], "gene": "http://reg.genome.network/gene/GN030220", "geneNCBI_id": 91869, "geneSymbol": "RFT1", "hgvs": [ "XM_011534215.3:c.1208+6825G>A" ], "proteinEffect": { "hgvs": "XP_011532517.1:n.1208+6825G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS551567" }, { "coordinates": [ { "allele": "A", "end": 1423, "referenceAllele": "G", "start": 1422 } ], "gene": "http://reg.genome.network/gene/GN030220", "geneNCBI_id": 91869, "geneSymbol": "RFT1", "hgvs": [ "XM_011534216.3:c.614G>A" ], "proteinEffect": { "hgvs": "XP_011532518.1:p.Arg205His", "hgvsWellDefined": "XP_011532518.1:p.Arg205His" }, "referenceSequence": "http://reg.genome.network/refseq/RS551568" }, { "coordinates": [ { "allele": "A", "end": 1337, "referenceAllele": "G", "start": 1336 } ], "gene": "http://reg.genome.network/gene/GN030220", "geneNCBI_id": 91869, "geneSymbol": "RFT1", "hgvs": [ "XM_017007460.1:c.1271G>A" ], "proteinEffect": { "hgvs": "XP_016862949.1:p.Arg424His", "hgvsWellDefined": "XP_016862949.1:p.Arg424His" }, "referenceSequence": "http://reg.genome.network/refseq/RS562219" }, { "coordinates": [ { "allele": "A", "end": 1509, "referenceAllele": "G", "start": 1508 } ], "gene": "http://reg.genome.network/gene/GN030220", "geneNCBI_id": 91869, "geneSymbol": "RFT1", "hgvs": [ "XM_017007461.2:c.614G>A" ], "proteinEffect": { "hgvs": "XP_016862950.1:p.Arg205His", "hgvsWellDefined": "XP_016862950.1:p.Arg205His" }, "referenceSequence": "http://reg.genome.network/refseq/RS562220" }, { "coordinates": [ { "allele": "A", "end": 1231, "referenceAllele": "G", "start": 1230 } ], "gene": "http://reg.genome.network/gene/GN030220", "geneNCBI_id": 91869, "geneSymbol": "RFT1", "hgvs": [ "XR_001740360.2:n.1231G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS590556" }, { "@id": "http://reg.genome.network/allele/PA2580493885", "coordinates": [ { "allele": "A", "end": 1306, "referenceAllele": "G", "start": 1305 } ], "gene": "http://reg.genome.network/gene/GN030220", "geneNCBI_id": 91869, "geneSymbol": "RFT1", "hgvs": [ "NM_052859.4:c.1271G>A" ], "proteinEffect": { "hgvs": "NP_443091.1:p.Arg424His", "hgvsWellDefined": "NP_443091.1:p.Arg424His" }, "referenceSequence": "http://reg.genome.network/refseq/RS671616", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000296292.8:c.1271G>A" }, "RefSeq": { "hgvs": "NM_052859.4:c.1271G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000296292.3:p.Arg424His" }, "RefSeq": { "hgvs": "NP_443091.1:p.Arg424His" } } } } ], "type": "nucleotide" }