{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA137376", "communityStandardTitle": [ "NM_022124.6(CDH23):c.3480G>T (p.Met1160Ile)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=55084[alleleid]", "alleleId": 55084, "preferredName": "NM_022124.6(CDH23):c.3480G>T (p.Met1160Ile)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/45919", "RCV": [ "RCV000039152", "RCV000891539", "RCV001105553", "RCV001105554" ], "variationId": 45919 } ], "ExAC": [ { "@id": "http://exac.broadinstitute.org/variant/10-73485178-G-T", "id": "10-73485178-G-T", "variant": "10:73485178 G / T" } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr10:g.73485178G>T?assembly=hg19", "id": "chr10:g.73485178G>T" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr10:g.71725421G>T?assembly=hg38", "id": "chr10:g.71725421G>T" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/111033519", "rs": 111033519 } ], "gnomAD_2": [ { "@id": "http://gnomad.broadinstitute.org/variant/10-73485178-G-T?dataset=gnomad_r2_1", "id": "10-73485178-G-T", "variant": "10:73485178 G / T" } ], "gnomAD_3": [ { "@id": "http://gnomad.broadinstitute.org/variant/10-71725421-G-T?dataset=gnomad_r3", "id": "10-71725421-G-T", "variant": "10:71725421 G / T" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/10-71725421-G-T?dataset=gnomad_r4", "id": "10-71725421-G-T", "variant": "10:71725421 G / T" } ] }, "genomicAlleles": [ { "chromosome": "10", "coordinates": [ { "allele": "T", "end": 71725421, "referenceAllele": "G", "start": 71725420 } ], "hgvs": [ "NC_000010.11:g.71725421G>T", "CM000672.2:g.71725421G>T" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000058" }, { "chromosome": "10", "coordinates": [ { "allele": "T", "end": 73485178, "referenceAllele": "G", "start": 73485177 } ], "hgvs": [ "NC_000010.10:g.73485178G>T", "CM000672.1:g.73485178G>T" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000034" }, { "chromosome": "10", "coordinates": [ { "allele": "T", "end": 73155184, "referenceAllele": "G", "start": 73155183 } ], "hgvs": [ "NC_000010.9:g.73155184G>T" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000010" }, { "coordinates": [ { "allele": "T", "end": 333475, "referenceAllele": "G", "start": 333474 } ], "hgvs": [ "NG_008835.1:g.333475G>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS001230" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "T", "end": 3884, "referenceAllele": "G", "start": 3883 } ], "gene": "http://reg.genome.network/gene/GN013733", "geneNCBI_id": 64072, "geneSymbol": "CDH23", "hgvs": [ "ENST00000224721.12:c.3480G>T" ], "proteinEffect": { "hgvs": "ENSP00000224721.9:p.Met1160Ile", "hgvsWellDefined": "ENSP00000224721.9:p.Met1160Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS740637", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000224721.12:c.3480G>T" }, "RefSeq": { "hgvs": "NM_022124.6:c.3480G>T" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000224721.9:p.Met1160Ile" }, "RefSeq": { "hgvs": "NP_071407.4:p.Met1160Ile" } } } }, { "coordinates": [ { "allele": "T", "end": 3867, "referenceAllele": "G", "start": 3866 } ], "gene": "http://reg.genome.network/gene/GN013733", "geneNCBI_id": 64072, "geneSymbol": "CDH23", "hgvs": [ "ENST00000398809.9:c.3477G>T" ], "proteinEffect": { "hgvs": "ENSP00000381789.5:p.Met1159Ile", "hgvsWellDefined": "ENSP00000381789.5:p.Met1159Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS753788" }, { "coordinates": [ { "allele": "T", "end": 3885, "referenceAllele": "G", "start": 3884 } ], "gene": "http://reg.genome.network/gene/GN013733", "geneNCBI_id": 64072, "geneSymbol": "CDH23", "hgvs": [ "ENST00000224721.10:c.3495G>T" ], "proteinEffect": { "hgvs": "ENSP00000224721.8:p.Met1165Ile", "hgvsWellDefined": "ENSP00000224721.8:p.Met1165Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS248471" }, { "coordinates": [ { "allele": "A", "end": 97, "endIntronDirection": "-", "endIntronOffset": 9078, "referenceAllele": "C", "start": 97, "startIntronDirection": "-", "startIntronOffset": 9079 } ], "gene": "http://reg.genome.network/gene/GN020304", "geneNCBI_id": 414152, "geneSymbol": "C10orf105", "hgvs": [ "ENST00000398786.2:c.-5-9079C>A" ], "proteinEffect": { "hgvs": "ENSP00000381766.3:n.-5-9079C>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS278418" }, { "coordinates": [ { "allele": "T", "end": 271, "endIntronDirection": "+", "endIntronOffset": 1316, "referenceAllele": "G", "start": 271, "startIntronDirection": "+", "startIntronOffset": 1315 } ], "gene": "http://reg.genome.network/gene/GN013733", "geneNCBI_id": 64072, "geneSymbol": "CDH23", "hgvs": [ "ENST00000398792.3:n.271+1316G>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS278420" }, { "coordinates": [ { "allele": "T", "end": 3867, "referenceAllele": "G", "start": 3866 } ], "gene": "http://reg.genome.network/gene/GN013733", "geneNCBI_id": 64072, "geneSymbol": "CDH23", "hgvs": [ "ENST00000398809.8:c.3477G>T" ], "proteinEffect": { "hgvs": "ENSP00000381789.5:p.Met1159Ile", "hgvsWellDefined": "ENSP00000381789.5:p.Met1159Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS278430" }, { "coordinates": [ { "allele": "T", "end": 3842, "referenceAllele": "G", "start": 3841 } ], "gene": "http://reg.genome.network/gene/GN013733", "geneNCBI_id": 64072, "geneSymbol": "CDH23", "hgvs": [ "ENST00000616684.4:c.3480G>T" ], "proteinEffect": { "hgvs": "ENSP00000482036.2:p.Met1160Ile", "hgvsWellDefined": "ENSP00000482036.2:p.Met1160Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS403156" }, { "coordinates": [ { "allele": "T", "end": 3870, "referenceAllele": "G", "start": 3869 } ], "gene": "http://reg.genome.network/gene/GN013733", "geneNCBI_id": 64072, "geneSymbol": "CDH23", "hgvs": [ "ENST00000622827.4:c.3480G>T" ], "proteinEffect": { "hgvs": "ENSP00000483211.1:p.Met1160Ile", "hgvsWellDefined": "ENSP00000483211.1:p.Met1160Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS405902" }, { "coordinates": [ { "allele": "A", "end": 97, "endIntronDirection": "-", "endIntronOffset": 9078, "referenceAllele": "C", "start": 97, "startIntronDirection": "-", "startIntronOffset": 9079 } ], "gene": "http://reg.genome.network/gene/GN020304", "geneNCBI_id": 414152, "geneSymbol": "C10orf105", "hgvs": [ "NM_001168390.1:c.-5-9079C>A" ], "proteinEffect": { "hgvs": "NP_001161862.1:n.-5-9079C>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS015107" }, { "@id": "http://reg.genome.network/allele/PA2826092860", "coordinates": [ { "allele": "T", "end": 3870, "referenceAllele": "G", "start": 3869 } ], "gene": "http://reg.genome.network/gene/GN013733", "geneNCBI_id": 64072, "geneSymbol": "CDH23", "hgvs": [ "NM_001171930.1:c.3480G>T" ], "proteinEffect": { "hgvs": "NP_001165401.1:p.Met1160Ile", "hgvsWellDefined": "NP_001165401.1:p.Met1160Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS015391" }, { "@id": "http://reg.genome.network/allele/PA137377", "coordinates": [ { "allele": "T", "end": 3870, "referenceAllele": "G", "start": 3869 } ], "gene": "http://reg.genome.network/gene/GN013733", "geneNCBI_id": 64072, "geneSymbol": "CDH23", "hgvs": [ "NM_022124.5:c.3480G>T" ], "proteinEffect": { "hgvs": "NP_071407.4:p.Met1160Ile", "hgvsWellDefined": "NP_071407.4:p.Met1160Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS037218" }, { "coordinates": [ { "allele": "T", "end": 3918, "referenceAllele": "G", "start": 3917 } ], "gene": "http://reg.genome.network/gene/GN013733", "geneNCBI_id": 64072, "geneSymbol": "CDH23", "hgvs": [ "XM_006717940.2:c.3675G>T" ], "proteinEffect": { "hgvs": "XP_006718003.1:p.Met1225Ile", "hgvsWellDefined": "XP_006718003.1:p.Met1225Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS072393" }, { "coordinates": [ { "allele": "T", "end": 3852, "referenceAllele": "G", "start": 3851 } ], "gene": "http://reg.genome.network/gene/GN013733", "geneNCBI_id": 64072, "geneSymbol": "CDH23", "hgvs": [ "XM_006717942.2:c.3609G>T" ], "proteinEffect": { "hgvs": "XP_006718005.1:p.Met1203Ile", "hgvsWellDefined": "XP_006718005.1:p.Met1203Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS072394" }, { "coordinates": [ { "allele": "A", "end": 787, "endIntronDirection": "+", "endIntronOffset": 986, "referenceAllele": "C", "start": 787, "startIntronDirection": "+", "startIntronOffset": 985 } ], "gene": "http://reg.genome.network/gene/GN020304", "geneNCBI_id": 414152, "geneSymbol": "C10orf105", "hgvs": [ "XM_011539810.1:c.-6+986C>A" ], "proteinEffect": { "hgvs": "XP_011538112.1:n.-6+986C>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS106760" }, { "coordinates": [ { "allele": "T", "end": 3918, "referenceAllele": "G", "start": 3917 } ], "gene": "http://reg.genome.network/gene/GN013733", "geneNCBI_id": 64072, "geneSymbol": "CDH23", "hgvs": [ "XM_011540039.1:c.3675G>T" ], "proteinEffect": { "hgvs": "XP_011538341.1:p.Met1225Ile", "hgvsWellDefined": "XP_011538341.1:p.Met1225Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS106989" }, { "coordinates": [ { "allele": "T", "end": 3912, "referenceAllele": "G", "start": 3911 } ], "gene": "http://reg.genome.network/gene/GN013733", "geneNCBI_id": 64072, "geneSymbol": "CDH23", "hgvs": [ "XM_011540040.1:c.3669G>T" ], "proteinEffect": { "hgvs": "XP_011538342.1:p.Met1223Ile", "hgvsWellDefined": "XP_011538342.1:p.Met1223Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS106990" }, { "coordinates": [ { "allele": "T", "end": 3870, "referenceAllele": "G", "start": 3869 } ], "gene": "http://reg.genome.network/gene/GN013733", "geneNCBI_id": 64072, "geneSymbol": "CDH23", "hgvs": [ "XM_011540041.1:c.3615G>T" ], "proteinEffect": { "hgvs": "XP_011538343.1:p.Met1205Ile", "hgvsWellDefined": "XP_011538343.1:p.Met1205Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS106991" }, { "coordinates": [ { "allele": "T", "end": 3918, "referenceAllele": "G", "start": 3917 } ], "gene": "http://reg.genome.network/gene/GN013733", "geneNCBI_id": 64072, "geneSymbol": "CDH23", "hgvs": [ "XM_011540042.1:c.3675G>T" ], "proteinEffect": { "hgvs": "XP_011538344.1:p.Met1225Ile", "hgvsWellDefined": "XP_011538344.1:p.Met1225Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS106992" }, { "coordinates": [ { "allele": "T", "end": 3918, "referenceAllele": "G", "start": 3917 } ], "gene": "http://reg.genome.network/gene/GN013733", "geneNCBI_id": 64072, "geneSymbol": "CDH23", "hgvs": [ "XM_011540043.1:c.3675G>T" ], "proteinEffect": { "hgvs": "XP_011538345.1:p.Met1225Ile", "hgvsWellDefined": "XP_011538345.1:p.Met1225Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS106993" }, { "coordinates": [ { "allele": "T", "end": 3602, "referenceAllele": "G", "start": 3601 } ], "gene": "http://reg.genome.network/gene/GN013733", "geneNCBI_id": 64072, "geneSymbol": "CDH23", "hgvs": [ "XM_011540044.1:c.3540G>T" ], "proteinEffect": { "hgvs": "XP_011538346.1:p.Met1180Ile", "hgvsWellDefined": "XP_011538346.1:p.Met1180Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS106994" }, { "coordinates": [ { "allele": "T", "end": 3918, "referenceAllele": "G", "start": 3917 } ], "gene": "http://reg.genome.network/gene/GN013733", "geneNCBI_id": 64072, "geneSymbol": "CDH23", "hgvs": [ "XM_011540045.1:c.3675G>T" ], "proteinEffect": { "hgvs": "XP_011538347.1:p.Met1225Ile", "hgvsWellDefined": "XP_011538347.1:p.Met1225Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS106995" }, { "coordinates": [ { "allele": "T", "end": 3340, "referenceAllele": "G", "start": 3339 } ], "gene": "http://reg.genome.network/gene/GN013733", "geneNCBI_id": 64072, "geneSymbol": "CDH23", "hgvs": [ "XM_011540046.1:c.3135G>T" ], "proteinEffect": { "hgvs": "XP_011538348.1:p.Met1045Ile", "hgvsWellDefined": "XP_011538348.1:p.Met1045Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS106996" }, { "coordinates": [ { "allele": "T", "end": 2508, "referenceAllele": "G", "start": 2507 } ], "gene": "http://reg.genome.network/gene/GN013733", "geneNCBI_id": 64072, "geneSymbol": "CDH23", "hgvs": [ "XM_011540047.1:c.2493G>T" ], "proteinEffect": { "hgvs": "XP_011538349.1:p.Met831Ile", "hgvsWellDefined": "XP_011538349.1:p.Met831Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS106997" }, { "coordinates": [ { "allele": "T", "end": 3918, "referenceAllele": "G", "start": 3917 } ], "gene": "http://reg.genome.network/gene/GN013733", "geneNCBI_id": 64072, "geneSymbol": "CDH23", "hgvs": [ "XM_011540048.1:c.3675G>T" ], "proteinEffect": { "hgvs": "XP_011538350.1:p.Met1225Ile", "hgvsWellDefined": "XP_011538350.1:p.Met1225Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS106998" }, { "coordinates": [ { "allele": "T", "end": 3918, "referenceAllele": "G", "start": 3917 } ], "gene": "http://reg.genome.network/gene/GN013733", "geneNCBI_id": 64072, "geneSymbol": "CDH23", "hgvs": [ "XM_011540049.1:c.3675G>T" ], "proteinEffect": { "hgvs": "XP_011538351.1:p.Met1225Ile", "hgvsWellDefined": "XP_011538351.1:p.Met1225Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS106999" }, { "coordinates": [ { "allele": "T", "end": 3918, "referenceAllele": "G", "start": 3917 } ], "gene": "http://reg.genome.network/gene/GN013733", "geneNCBI_id": 64072, "geneSymbol": "CDH23", "hgvs": [ "XM_011540050.1:c.3675G>T" ], "proteinEffect": { "hgvs": "XP_011538352.1:p.Met1225Ile", "hgvsWellDefined": "XP_011538352.1:p.Met1225Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS107000" }, { "coordinates": [ { "allele": "T", "end": 3918, "referenceAllele": "G", "start": 3917 } ], "gene": "http://reg.genome.network/gene/GN013733", "geneNCBI_id": 64072, "geneSymbol": "CDH23", "hgvs": [ "XM_011540051.1:c.3675G>T" ], "proteinEffect": { "hgvs": "XP_011538353.1:p.Met1225Ile", "hgvsWellDefined": "XP_011538353.1:p.Met1225Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS107001" }, { "coordinates": [ { "allele": "T", "end": 141, "referenceAllele": "G", "start": 140 } ], "gene": "http://reg.genome.network/gene/GN013733", "geneNCBI_id": 64072, "geneSymbol": "CDH23", "hgvs": [ "XM_011540052.1:c.3G>T" ], "proteinEffect": { "hgvs": "XP_011538354.1:p.Met1Ile", "hgvsWellDefined": "XP_011538354.1:p.Met1Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS107002" }, { "coordinates": [ { "allele": "T", "end": 3918, "referenceAllele": "G", "start": 3917 } ], "gene": "http://reg.genome.network/gene/GN013733", "geneNCBI_id": 64072, "geneSymbol": "CDH23", "hgvs": [ "XM_011540053.1:c.3675G>T" ], "proteinEffect": { "hgvs": "XP_011538355.1:p.Met1225Ile", "hgvsWellDefined": "XP_011538355.1:p.Met1225Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS107003" }, { "coordinates": [ { "allele": "T", "end": 3918, "referenceAllele": "G", "start": 3917 } ], "gene": "http://reg.genome.network/gene/GN013733", "geneNCBI_id": 64072, "geneSymbol": "CDH23", "hgvs": [ "XR_945796.1:n.3918G>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS139429" }, { "coordinates": [ { "allele": "A", "end": 123, "endIntronDirection": "-", "endIntronOffset": 9078, "referenceAllele": "C", "start": 123, "startIntronDirection": "-", "startIntronOffset": 9079 } ], "gene": "http://reg.genome.network/gene/GN020304", "geneNCBI_id": 414152, "geneSymbol": "C10orf105", "hgvs": [ "NM_001168390.2:c.-5-9079C>A" ], "proteinEffect": { "hgvs": "NP_001161862.1:n.-5-9079C>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS678588" }, { "@id": "http://reg.genome.network/allele/PA2826092860", "coordinates": [ { "allele": "T", "end": 3884, "referenceAllele": "G", "start": 3883 } ], "gene": "http://reg.genome.network/gene/GN013733", "geneNCBI_id": 64072, "geneSymbol": "CDH23", "hgvs": [ "NM_001171930.2:c.3480G>T" ], "proteinEffect": { "hgvs": "NP_001165401.1:p.Met1160Ile", "hgvsWellDefined": "NP_001165401.1:p.Met1160Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS678723" }, { "@id": "http://reg.genome.network/allele/PA137377", "coordinates": [ { "allele": "T", "end": 3884, "referenceAllele": "G", "start": 3883 } ], "gene": "http://reg.genome.network/gene/GN013733", "geneNCBI_id": 64072, "geneSymbol": "CDH23", "hgvs": [ "NM_022124.6:c.3480G>T" ], "proteinEffect": { "hgvs": "NP_071407.4:p.Met1160Ile", "hgvsWellDefined": "NP_071407.4:p.Met1160Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS698509", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000224721.12:c.3480G>T" }, "RefSeq": { "hgvs": "NM_022124.6:c.3480G>T" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000224721.9:p.Met1160Ile" }, "RefSeq": { "hgvs": "NP_071407.4:p.Met1160Ile" } } } } ], "type": "nucleotide" }