{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA2147704", "communityStandardTitle": [ "NM_000091.5(COL4A3):c.4996A>G (p.Met1666Val)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=962692[alleleid]", "alleleId": 962692, "preferredName": "NM_000091.5(COL4A3):c.4996A>G (p.Met1666Val)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/974509", "RCV": [ "RCV001316984", "RCV001281281", "RCV001836251" ], "variationId": 974509 } ], "ExAC": [ { "@id": "http://exac.broadinstitute.org/variant/2-228176569-A-G", "id": "2-228176569-A-G", "variant": "2:228176569 A / G" } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr2:g.228176569A>G?assembly=hg19", "id": "chr2:g.228176569A>G" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr2:g.227311853A>G?assembly=hg38", "id": "chr2:g.227311853A>G" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/759583948", "rs": 759583948 } ], "gnomAD_2": [ { "@id": "http://gnomad.broadinstitute.org/variant/2-228176569-A-G?dataset=gnomad_r2_1", "id": "2-228176569-A-G", "variant": "2:228176569 A / G" } ], "gnomAD_3": [ { "@id": "http://gnomad.broadinstitute.org/variant/2-227311853-A-G?dataset=gnomad_r3", "id": "2-227311853-A-G", "variant": "2:227311853 A / G" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/2-227311853-A-G?dataset=gnomad_r4", "id": "2-227311853-A-G", "variant": "2:227311853 A / G" } ] }, "genomicAlleles": [ { "chromosome": "2", "coordinates": [ { "allele": "G", "end": 227311853, "referenceAllele": "A", "start": 227311852 } ], "hgvs": [ "NC_000002.12:g.227311853A>G", "CM000664.2:g.227311853A>G" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000050" }, { "chromosome": "2", "coordinates": [ { "allele": "G", "end": 228176569, "referenceAllele": "A", "start": 228176568 } ], "hgvs": [ "NC_000002.11:g.228176569A>G", "CM000664.1:g.228176569A>G" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000026" }, { "chromosome": "2", "coordinates": [ { "allele": "G", "end": 227884813, "referenceAllele": "A", "start": 227884812 } ], "hgvs": [ "NC_000002.10:g.227884813A>G" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000002" }, { "coordinates": [ { "allele": "G", "end": 152289, "referenceAllele": "A", "start": 152288 } ], "hgvs": [ "NG_011591.1:g.152289A>G", "LRG_230:g.152289A>G" ], "referenceSequence": "http://reg.genome.network/refseq/RS001839" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "G", "end": 2254, "referenceAllele": "A", "start": 2253 } ], "gene": "http://reg.genome.network/gene/GN002204", "geneNCBI_id": 1285, "geneSymbol": "COL4A3", "hgvs": [ "ENST00000471862.2:n.2254A>G" ], "referenceSequence": "http://reg.genome.network/refseq/RS825223" }, { "coordinates": [ { "allele": "G", "end": 218, "referenceAllele": "A", "start": 217 } ], "gene": "http://reg.genome.network/gene/GN002204", "geneNCBI_id": 1285, "geneSymbol": "COL4A3", "hgvs": [ "ENST00000682257.1:n.218A>G" ], "referenceSequence": "http://reg.genome.network/refseq/RS827252" }, { "coordinates": [ { "allele": "G", "end": 294, "referenceAllele": "A", "start": 293 } ], "gene": "http://reg.genome.network/gene/GN002204", "geneNCBI_id": 1285, "geneSymbol": "COL4A3", "hgvs": [ "ENST00000682970.1:n.294A>G" ], "referenceSequence": "http://reg.genome.network/refseq/RS827958" }, { "coordinates": [ { "allele": "G", "end": 1935, "referenceAllele": "A", "start": 1934 } ], "gene": "http://reg.genome.network/gene/GN002204", "geneNCBI_id": 1285, "geneSymbol": "COL4A3", "hgvs": [ "ENST00000683077.1:n.1935A>G" ], "referenceSequence": "http://reg.genome.network/refseq/RS828062" }, { "coordinates": [ { "allele": "G", "end": 2563, "referenceAllele": "A", "start": 2562 } ], "gene": "http://reg.genome.network/gene/GN002204", "geneNCBI_id": 1285, "geneSymbol": "COL4A3", "hgvs": [ "ENST00000684413.1:n.2563A>G" ], "referenceSequence": "http://reg.genome.network/refseq/RS829368" }, { "coordinates": [ { "allele": "G", "end": 417, "referenceAllele": "A", "start": 416 } ], "gene": "http://reg.genome.network/gene/GN002204", "geneNCBI_id": 1285, "geneSymbol": "COL4A3", "hgvs": [ "ENST00000684724.1:n.417A>G" ], "referenceSequence": "http://reg.genome.network/refseq/RS829675" }, { "coordinates": [ { "allele": "G", "end": 5099, "referenceAllele": "A", "start": 5098 } ], "gene": "http://reg.genome.network/gene/GN002204", "geneNCBI_id": 1285, "geneSymbol": "COL4A3", "hgvs": [ "ENST00000396578.8:c.4996A>G" ], "proteinEffect": { "hgvs": "ENSP00000379823.3:p.Met1666Val", "hgvsWellDefined": "ENSP00000379823.3:p.Met1666Val" }, "referenceSequence": "http://reg.genome.network/refseq/RS753536", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000396578.8:c.4996A>G" }, "RefSeq": { "hgvs": "NM_000091.5:c.4996A>G" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000379823.3:p.Met1666Val" }, "RefSeq": { "hgvs": "NP_000082.2:p.Met1666Val" } } } }, { "coordinates": [ { "allele": "G", "end": 789, "referenceAllele": "A", "start": 788 } ], "gene": "http://reg.genome.network/gene/GN002204", "geneNCBI_id": 1285, "geneSymbol": "COL4A3", "hgvs": [ "ENST00000469504.2:c.789A>G" ], "proteinEffect": { "hgvs": "ENSP00000493493.1:n.789A>G" }, "referenceSequence": "http://reg.genome.network/refseq/RS756974" }, { "coordinates": [ { "allele": "G", "end": 509, "referenceAllele": "A", "start": 508 } ], "gene": "http://reg.genome.network/gene/GN002204", "geneNCBI_id": 1285, "geneSymbol": "COL4A3", "hgvs": [ "ENST00000643388.1:c.509A>G" ], "proteinEffect": { "hgvs": "ENSP00000495177.1:p.His170Arg", "hgvsWellDefined": "ENSP00000495177.1:p.His170Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS767256" }, { "coordinates": [ { "allele": "G", "end": 5158, "referenceAllele": "A", "start": 5157 } ], "gene": "http://reg.genome.network/gene/GN002204", "geneNCBI_id": 1285, "geneSymbol": "COL4A3", "hgvs": [ "ENST00000396578.7:c.4996A>G" ], "proteinEffect": { "hgvs": "ENSP00000379823.3:p.Met1666Val", "hgvsWellDefined": "ENSP00000379823.3:p.Met1666Val" }, "referenceSequence": "http://reg.genome.network/refseq/RS277337" }, { "coordinates": [ { "allele": "G", "end": 504, "referenceAllele": "A", "start": 503 } ], "gene": "http://reg.genome.network/gene/GN002204", "geneNCBI_id": 1285, "geneSymbol": "COL4A3", "hgvs": [ "ENST00000469504.1:n.504A>G" ], "referenceSequence": "http://reg.genome.network/refseq/RS312173" }, { "@id": "http://reg.genome.network/allele/PA1139696836", "coordinates": [ { "allele": "G", "end": 5158, "referenceAllele": "A", "start": 5157 } ], "gene": "http://reg.genome.network/gene/GN002204", "geneNCBI_id": 1285, "geneSymbol": "COL4A3", "hgvs": [ "NM_000091.4:c.4996A>G", "LRG_230t1:c.4996A>G" ], "proteinEffect": { "hgvs": "NP_000082.2:p.Met1666Val", "hgvsWellDefined": "NP_000082.2:p.Met1666Val" }, "referenceSequence": "http://reg.genome.network/refseq/RS006155" }, { "coordinates": [ { "allele": "C", "end": 47, "endIntronDirection": "-", "endIntronOffset": 6197, "referenceAllele": "T", "start": 47, "startIntronDirection": "-", "startIntronOffset": 6198 } ], "gene": "http://reg.genome.network/gene/GN041067", "geneNCBI_id": 654841, "geneSymbol": "MFF-DT", "hgvs": [ "NR_102371.1:n.48-6198T>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS052797" }, { "coordinates": [ { "allele": "G", "end": 4961, "referenceAllele": "A", "start": 4960 } ], "gene": "http://reg.genome.network/gene/GN002204", "geneNCBI_id": 1285, "geneSymbol": "COL4A3", "hgvs": [ "XM_005246276.2:c.4823A>G" ], "proteinEffect": { "hgvs": "XP_005246333.1:p.His1608Arg", "hgvsWellDefined": "XP_005246333.1:p.His1608Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS057548" }, { "coordinates": [ { "allele": "G", "end": 5029, "referenceAllele": "A", "start": 5028 } ], "gene": "http://reg.genome.network/gene/GN002204", "geneNCBI_id": 1285, "geneSymbol": "COL4A3", "hgvs": [ "XM_005246277.2:c.4891A>G" ], "proteinEffect": { "hgvs": "XP_005246334.1:p.Met1631Val", "hgvsWellDefined": "XP_005246334.1:p.Met1631Val" }, "referenceSequence": "http://reg.genome.network/refseq/RS057549" }, { "coordinates": [ { "allele": "G", "end": 4190, "referenceAllele": "A", "start": 4189 } ], "gene": "http://reg.genome.network/gene/GN002204", "geneNCBI_id": 1285, "geneSymbol": "COL4A3", "hgvs": [ "XM_011510556.1:c.3757A>G" ], "proteinEffect": { "hgvs": "XP_011508858.1:p.Met1253Val", "hgvsWellDefined": "XP_011508858.1:p.Met1253Val" }, "referenceSequence": "http://reg.genome.network/refseq/RS077819" }, { "coordinates": [ { "allele": "G", "end": 4956, "referenceAllele": "A", "start": 4955 } ], "gene": "http://reg.genome.network/gene/GN002204", "geneNCBI_id": 1285, "geneSymbol": "COL4A3", "hgvs": [ "XR_241280.2:n.4956A>G" ], "referenceSequence": "http://reg.genome.network/refseq/RS116013" }, { "coordinates": [ { "allele": "G", "end": 5029, "referenceAllele": "A", "start": 5028 } ], "gene": "http://reg.genome.network/gene/GN002204", "geneNCBI_id": 1285, "geneSymbol": "COL4A3", "hgvs": [ "XM_005246277.3:c.4891A>G" ], "proteinEffect": { "hgvs": "XP_005246334.1:p.Met1631Val", "hgvsWellDefined": "XP_005246334.1:p.Met1631Val" }, "referenceSequence": "http://reg.genome.network/refseq/RS532574" }, { "coordinates": [ { "allele": "G", "end": 4190, "referenceAllele": "A", "start": 4189 } ], "gene": "http://reg.genome.network/gene/GN002204", "geneNCBI_id": 1285, "geneSymbol": "COL4A3", "hgvs": [ "XM_011510556.2:c.3757A>G" ], "proteinEffect": { "hgvs": "XP_011508858.1:p.Met1253Val", "hgvsWellDefined": "XP_011508858.1:p.Met1253Val" }, "referenceSequence": "http://reg.genome.network/refseq/RS541765" }, { "coordinates": [ { "allele": "G", "end": 4956, "referenceAllele": "A", "start": 4955 } ], "gene": "http://reg.genome.network/gene/GN002204", "geneNCBI_id": 1285, "geneSymbol": "COL4A3", "hgvs": [ "XR_241280.3:n.4956A>G" ], "referenceSequence": "http://reg.genome.network/refseq/RS605830" }, { "@id": "http://reg.genome.network/allele/PA1139696836", "coordinates": [ { "allele": "G", "end": 5099, "referenceAllele": "A", "start": 5098 } ], "gene": "http://reg.genome.network/gene/GN002204", "geneNCBI_id": 1285, "geneSymbol": "COL4A3", "hgvs": [ "NM_000091.5:c.4996A>G" ], "proteinEffect": { "hgvs": "NP_000082.2:p.Met1666Val", "hgvsWellDefined": "NP_000082.2:p.Met1666Val" }, "referenceSequence": "http://reg.genome.network/refseq/RS674698", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000396578.8:c.4996A>G" }, "RefSeq": { "hgvs": "NM_000091.5:c.4996A>G" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000379823.3:p.Met1666Val" }, "RefSeq": { "hgvs": "NP_000082.2:p.Met1666Val" } } } } ], "type": "nucleotide" }