{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA669498", "communityStandardTitle": [ "NM_005529.7(HSPG2):c.12221G>A (p.Arg4074His)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=863580[alleleid]", "alleleId": 863580, "preferredName": "NM_005529.7(HSPG2):c.12221G>A (p.Arg4074His)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/875572", "RCV": [ "RCV001099540", "RCV001099541", "RCV001873488", "RCV002556016" ], "variationId": 875572 } ], "ExAC": [ { "@id": "http://exac.broadinstitute.org/variant/1-22155344-C-T", "id": "1-22155344-C-T", "variant": "1:22155344 C / T" } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr1:g.22155344C>T?assembly=hg19", "id": "chr1:g.22155344C>T" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr1:g.21828851C>T?assembly=hg38", "id": "chr1:g.21828851C>T" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/376190109", "rs": 376190109 } ], "gnomAD_2": [ { "@id": "http://gnomad.broadinstitute.org/variant/1-22155344-C-T?dataset=gnomad_r2_1", "id": "1-22155344-C-T", "variant": "1:22155344 C / T" } ], "gnomAD_3": [ { "@id": "http://gnomad.broadinstitute.org/variant/1-21828851-C-T?dataset=gnomad_r3", "id": "1-21828851-C-T", "variant": "1:21828851 C / T" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/1-21828851-C-T?dataset=gnomad_r4", "id": "1-21828851-C-T", "variant": "1:21828851 C / T" } ] }, "genomicAlleles": [ { "chromosome": "1", "coordinates": [ { "allele": "T", "end": 21828851, "referenceAllele": "C", "start": 21828850 } ], "hgvs": [ "NC_000001.11:g.21828851C>T", "CM000663.2:g.21828851C>T" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000049" }, { "chromosome": "1", "coordinates": [ { "allele": "T", "end": 22155344, "referenceAllele": "C", "start": 22155343 } ], "hgvs": [ "NC_000001.10:g.22155344C>T", "CM000663.1:g.22155344C>T" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000025" }, { "chromosome": "1", "coordinates": [ { "allele": "T", "end": 22027931, "referenceAllele": "C", "start": 22027930 } ], "hgvs": [ "NC_000001.9:g.22027931C>T" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000001" }, { "coordinates": [ { "allele": "A", "end": 113407, "referenceAllele": "G", "start": 113406 } ], "hgvs": [ "NG_016740.1:g.113407G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS003265" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 12314, "referenceAllele": "G", "start": 12313 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "ENST00000374695.8:c.12221G>A" ], "proteinEffect": { "hgvs": "ENSP00000363827.3:p.Arg4074His", "hgvsWellDefined": "ENSP00000363827.3:p.Arg4074His" }, "referenceSequence": "http://reg.genome.network/refseq/RS751480", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000374695.8:c.12221G>A" }, "RefSeq": { "hgvs": "NM_005529.7:c.12221G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000363827.3:p.Arg4074His" }, "RefSeq": { "hgvs": "NP_005520.4:p.Arg4074His" } } } }, { "coordinates": [ { "allele": "A", "end": 12301, "referenceAllele": "G", "start": 12300 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "ENST00000374695.7:c.12221G>A" ], "proteinEffect": { "hgvs": "ENSP00000363827.3:p.Arg4074His", "hgvsWellDefined": "ENSP00000363827.3:p.Arg4074His" }, "referenceSequence": "http://reg.genome.network/refseq/RS270365" }, { "coordinates": [ { "allele": "A", "end": 1560, "referenceAllele": "G", "start": 1559 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "ENST00000486901.1:n.1560G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS325595" }, { "@id": "http://reg.genome.network/allele/PA1139697616", "coordinates": [ { "allele": "A", "end": 12304, "referenceAllele": "G", "start": 12303 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "NM_001291860.1:c.12224G>A" ], "proteinEffect": { "hgvs": "NP_001278789.1:p.Arg4075His", "hgvsWellDefined": "NP_001278789.1:p.Arg4075His" }, "referenceSequence": "http://reg.genome.network/refseq/RS024346" }, { "@id": "http://reg.genome.network/allele/PA2829596376", "coordinates": [ { "allele": "A", "end": 12301, "referenceAllele": "G", "start": 12300 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "NM_005529.6:c.12221G>A" ], "proteinEffect": { "hgvs": "NP_005520.4:p.Arg4074His", "hgvsWellDefined": "NP_005520.4:p.Arg4074His" }, "referenceSequence": "http://reg.genome.network/refseq/RS030620" }, { "coordinates": [ { "allele": "A", "end": 12800, "referenceAllele": "G", "start": 12799 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_006710594.2:c.12785G>A" ], "proteinEffect": { "hgvs": "XP_006710657.1:p.Arg4262His", "hgvsWellDefined": "XP_006710657.1:p.Arg4262His" }, "referenceSequence": "http://reg.genome.network/refseq/RS068699" }, { "coordinates": [ { "allele": "A", "end": 12752, "referenceAllele": "G", "start": 12751 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_006710595.2:c.12737G>A" ], "proteinEffect": { "hgvs": "XP_006710658.1:p.Arg4246His", "hgvsWellDefined": "XP_006710658.1:p.Arg4246His" }, "referenceSequence": "http://reg.genome.network/refseq/RS068700" }, { "coordinates": [ { "allele": "A", "end": 12731, "referenceAllele": "G", "start": 12730 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_006710596.2:c.12716G>A" ], "proteinEffect": { "hgvs": "XP_006710659.1:p.Arg4239His", "hgvsWellDefined": "XP_006710659.1:p.Arg4239His" }, "referenceSequence": "http://reg.genome.network/refseq/RS068701" }, { "coordinates": [ { "allele": "A", "end": 12254, "referenceAllele": "G", "start": 12253 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_006710597.2:c.12239G>A" ], "proteinEffect": { "hgvs": "XP_006710660.1:p.Arg4080His", "hgvsWellDefined": "XP_006710660.1:p.Arg4080His" }, "referenceSequence": "http://reg.genome.network/refseq/RS068702" }, { "coordinates": [ { "allele": "A", "end": 12803, "referenceAllele": "G", "start": 12802 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_011541317.1:c.12788G>A" ], "proteinEffect": { "hgvs": "XP_011539619.1:p.Arg4263His", "hgvsWellDefined": "XP_011539619.1:p.Arg4263His" }, "referenceSequence": "http://reg.genome.network/refseq/RS108259" }, { "coordinates": [ { "allele": "A", "end": 12785, "referenceAllele": "G", "start": 12784 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_011541318.1:c.12770G>A" ], "proteinEffect": { "hgvs": "XP_011539620.1:p.Arg4257His", "hgvsWellDefined": "XP_011539620.1:p.Arg4257His" }, "referenceSequence": "http://reg.genome.network/refseq/RS108260" }, { "coordinates": [ { "allele": "A", "end": 12803, "referenceAllele": "G", "start": 12802 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_011541319.1:c.12788G>A" ], "proteinEffect": { "hgvs": "XP_011539621.1:p.Arg4263His", "hgvsWellDefined": "XP_011539621.1:p.Arg4263His" }, "referenceSequence": "http://reg.genome.network/refseq/RS108261" }, { "coordinates": [ { "allele": "A", "end": 12524, "referenceAllele": "G", "start": 12523 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_011541320.1:c.12509G>A" ], "proteinEffect": { "hgvs": "XP_011539622.1:p.Arg4170His", "hgvsWellDefined": "XP_011539622.1:p.Arg4170His" }, "referenceSequence": "http://reg.genome.network/refseq/RS108262" }, { "coordinates": [ { "allele": "A", "end": 12308, "referenceAllele": "G", "start": 12307 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_011541321.1:c.12293G>A" ], "proteinEffect": { "hgvs": "XP_011539623.1:p.Arg4098His", "hgvsWellDefined": "XP_011539623.1:p.Arg4098His" }, "referenceSequence": "http://reg.genome.network/refseq/RS108263" }, { "coordinates": [ { "allele": "A", "end": 12785, "referenceAllele": "G", "start": 12784 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_011541318.2:c.12770G>A" ], "proteinEffect": { "hgvs": "XP_011539620.1:p.Arg4257His", "hgvsWellDefined": "XP_011539620.1:p.Arg4257His" }, "referenceSequence": "http://reg.genome.network/refseq/RS554390" }, { "coordinates": [ { "allele": "A", "end": 12431, "referenceAllele": "G", "start": 12430 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_017001120.1:c.12416G>A" ], "proteinEffect": { "hgvs": "XP_016856609.1:p.Arg4139His", "hgvsWellDefined": "XP_016856609.1:p.Arg4139His" }, "referenceSequence": "http://reg.genome.network/refseq/RS557347" }, { "coordinates": [ { "allele": "A", "end": 12380, "referenceAllele": "G", "start": 12379 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_017001121.1:c.12365G>A" ], "proteinEffect": { "hgvs": "XP_016856610.1:p.Arg4122His", "hgvsWellDefined": "XP_016856610.1:p.Arg4122His" }, "referenceSequence": "http://reg.genome.network/refseq/RS557348" }, { "coordinates": [ { "allele": "A", "end": 12377, "referenceAllele": "G", "start": 12376 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_017001122.1:c.12362G>A" ], "proteinEffect": { "hgvs": "XP_016856611.1:p.Arg4121His", "hgvsWellDefined": "XP_016856611.1:p.Arg4121His" }, "referenceSequence": "http://reg.genome.network/refseq/RS557349" }, { "@id": "http://reg.genome.network/allele/PA2829596376", "coordinates": [ { "allele": "A", "end": 12314, "referenceAllele": "G", "start": 12313 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "NM_005529.7:c.12221G>A" ], "proteinEffect": { "hgvs": "NP_005520.4:p.Arg4074His", "hgvsWellDefined": "NP_005520.4:p.Arg4074His" }, "referenceSequence": "http://reg.genome.network/refseq/RS667014", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000374695.8:c.12221G>A" }, "RefSeq": { "hgvs": "NM_005529.7:c.12221G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000363827.3:p.Arg4074His" }, "RefSeq": { "hgvs": "NP_005520.4:p.Arg4074His" } } } }, { "@id": "http://reg.genome.network/allele/PA1139697616", "coordinates": [ { "allele": "A", "end": 12317, "referenceAllele": "G", "start": 12316 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "NM_001291860.2:c.12224G>A" ], "proteinEffect": { "hgvs": "NP_001278789.1:p.Arg4075His", "hgvsWellDefined": "NP_001278789.1:p.Arg4075His" }, "referenceSequence": "http://reg.genome.network/refseq/RS682883" } ], "type": "nucleotide" }