{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA10068114", "communityStandardTitle": [ "NM_001379500.1(COL18A1):c.3851G>A (p.Arg1284His)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=1523549[alleleid]", "alleleId": 1523549, "preferredName": "NM_001379500.1(COL18A1):c.3851G>A (p.Arg1284His)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/1601603", "RCV": [ "RCV002127372", "RCV004553760" ], "variationId": 1601603 } ], "ExAC": [ { "@id": "http://exac.broadinstitute.org/variant/21-46932143-G-A", "id": "21-46932143-G-A", "variant": "21:46932143 G / A" } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr21:g.46932143G>A?assembly=hg19", "id": "chr21:g.46932143G>A" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr21:g.45512229G>A?assembly=hg38", "id": "chr21:g.45512229G>A" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/202049650", "rs": 202049650 } ], "gnomAD_2": [ { "@id": "http://gnomad.broadinstitute.org/variant/21-46932143-G-A?dataset=gnomad_r2_1", "id": "21-46932143-G-A", "variant": "21:46932143 G / A" } ], "gnomAD_3": [ { "@id": "http://gnomad.broadinstitute.org/variant/21-45512229-G-A?dataset=gnomad_r3", "id": "21-45512229-G-A", "variant": "21:45512229 G / A" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/21-45512229-G-A?dataset=gnomad_r4", "id": "21-45512229-G-A", "variant": "21:45512229 G / A" } ] }, "genomicAlleles": [ { "chromosome": "21", "coordinates": [ { "allele": "A", "end": 45512229, "referenceAllele": "G", "start": 45512228 } ], "hgvs": [ "NC_000021.9:g.45512229G>A", "CM000683.2:g.45512229G>A" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000069" }, { "chromosome": "21", "coordinates": [ { "allele": "A", "end": 46932143, "referenceAllele": "G", "start": 46932142 } ], "hgvs": [ "NC_000021.8:g.46932143G>A", "CM000683.1:g.46932143G>A" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000045" }, { "chromosome": "21", "coordinates": [ { "allele": "A", "end": 45756571, "referenceAllele": "G", "start": 45756570 } ], "hgvs": [ "NC_000021.7:g.45756571G>A" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000021" }, { "coordinates": [ { "allele": "A", "end": 112038, "referenceAllele": "G", "start": 112037 } ], "hgvs": [ "NG_011903.1:g.112038G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS002052" }, { "coordinates": [ { "allele": "T", "end": 55915, "referenceAllele": "C", "start": 55914 } ], "hgvs": [ "NG_028278.2:g.55915C>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS616290" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 4400, "referenceAllele": "G", "start": 4399 } ], "gene": "http://reg.genome.network/gene/GN002195", "geneNCBI_id": 80781, "geneSymbol": "COL18A1", "hgvs": [ "ENST00000355480.10:c.4391G>A" ], "proteinEffect": { "hgvs": "ENSP00000347665.5:p.Arg1464His", "hgvsWellDefined": "ENSP00000347665.5:p.Arg1464His" }, "referenceSequence": "http://reg.genome.network/refseq/RS748674" }, { "coordinates": [ { "allele": "A", "end": 3917, "referenceAllele": "G", "start": 3916 } ], "gene": "http://reg.genome.network/gene/GN002195", "geneNCBI_id": 80781, "geneSymbol": "COL18A1", "hgvs": [ "ENST00000651438.1:c.3851G>A" ], "proteinEffect": { "hgvs": "ENSP00000498485.1:p.Arg1284His", "hgvsWellDefined": "ENSP00000498485.1:p.Arg1284His" }, "referenceSequence": "http://reg.genome.network/refseq/RS771668", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000651438.1:c.3851G>A" }, "RefSeq": { "hgvs": "NM_001379500.1:c.3851G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000498485.1:p.Arg1284His" }, "RefSeq": { "hgvs": "NP_001366429.1:p.Arg1284His" } } } }, { "coordinates": [ { "allele": "A", "end": 1895, "referenceAllele": "G", "start": 1894 } ], "gene": "http://reg.genome.network/gene/GN002195", "geneNCBI_id": 80781, "geneSymbol": "COL18A1", "hgvs": [ "ENST00000342220.9:c.1895G>A" ], "proteinEffect": { "hgvs": "ENSP00000339118.5:p.Arg632His", "hgvsWellDefined": "ENSP00000339118.5:p.Arg632His" }, "referenceSequence": "http://reg.genome.network/refseq/RS261507" }, { "coordinates": [ { "allele": "A", "end": 4433, "referenceAllele": "G", "start": 4432 } ], "gene": "http://reg.genome.network/gene/GN002195", "geneNCBI_id": 80781, "geneSymbol": "COL18A1", "hgvs": [ "ENST00000355480.9:c.4391G>A" ], "proteinEffect": { "hgvs": "ENSP00000347665.5:p.Arg1464His", "hgvsWellDefined": "ENSP00000347665.5:p.Arg1464His" }, "referenceSequence": "http://reg.genome.network/refseq/RS263444" }, { "coordinates": [ { "allele": "A", "end": 5096, "referenceAllele": "G", "start": 5095 } ], "gene": "http://reg.genome.network/gene/GN002195", "geneNCBI_id": 80781, "geneSymbol": "COL18A1", "hgvs": [ "ENST00000359759.8:c.5096G>A" ], "proteinEffect": { "hgvs": "ENSP00000352798.4:p.Arg1699His", "hgvsWellDefined": "ENSP00000352798.4:p.Arg1699His" }, "referenceSequence": "http://reg.genome.network/refseq/RS264897" }, { "coordinates": [ { "allele": "A", "end": 3945, "referenceAllele": "G", "start": 3944 } ], "gene": "http://reg.genome.network/gene/GN002195", "geneNCBI_id": 80781, "geneSymbol": "COL18A1", "hgvs": [ "ENST00000400337.6:c.3851G>A" ], "proteinEffect": { "hgvs": "ENSP00000383191.2:p.Arg1284His", "hgvsWellDefined": "ENSP00000383191.2:p.Arg1284His" }, "referenceSequence": "http://reg.genome.network/refseq/RS278999" }, { "coordinates": [ { "allele": "T", "end": 497, "endIntronDirection": "+", "endIntronOffset": 13588, "referenceAllele": "C", "start": 497, "startIntronDirection": "+", "startIntronOffset": 13587 } ], "gene": "http://reg.genome.network/gene/GN010937", "geneNCBI_id": 6573, "geneSymbol": "SLC19A1", "hgvs": [ "ENST00000417954.5:c.497+13588C>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS285163" }, { "coordinates": [ { "allele": "A", "end": 805, "referenceAllele": "G", "start": 804 } ], "gene": "http://reg.genome.network/gene/GN002195", "geneNCBI_id": 80781, "geneSymbol": "COL18A1", "hgvs": [ "ENST00000423214.1:c.805G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS287647" }, { "coordinates": [ { "allele": "A", "end": 2177, "referenceAllele": "G", "start": 2176 } ], "gene": "http://reg.genome.network/gene/GN002195", "geneNCBI_id": 80781, "geneSymbol": "COL18A1", "hgvs": [ "ENST00000473212.1:n.2177G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS315017" }, { "coordinates": [ { "allele": "T", "end": 1617, "endIntronDirection": "+", "endIntronOffset": 13588, "referenceAllele": "C", "start": 1617, "startIntronDirection": "+", "startIntronOffset": 13587 } ], "gene": "http://reg.genome.network/gene/GN010937", "geneNCBI_id": 6573, "geneSymbol": "SLC19A1", "hgvs": [ "ENST00000567670.5:c.1293+13588C>T" ], "proteinEffect": { "hgvs": "ENSP00000457278.1:n.1293+13588C>T" }, "referenceSequence": "http://reg.genome.network/refseq/RS380264" }, { "@id": "http://reg.genome.network/allele/PA2830036660", "coordinates": [ { "allele": "A", "end": 4403, "referenceAllele": "G", "start": 4402 } ], "gene": "http://reg.genome.network/gene/GN002195", "geneNCBI_id": 80781, "geneSymbol": "COL18A1", "hgvs": [ "NM_030582.3:c.4382G>A" ], "proteinEffect": { "hgvs": "NP_085059.2:p.Arg1461His", "hgvsWellDefined": "NP_085059.2:p.Arg1461His" }, "referenceSequence": "http://reg.genome.network/refseq/RS038334" }, { "@id": "http://reg.genome.network/allele/PA2573296684", "coordinates": [ { "allele": "A", "end": 5108, "referenceAllele": "G", "start": 5107 } ], "gene": "http://reg.genome.network/gene/GN002195", "geneNCBI_id": 80781, "geneSymbol": "COL18A1", "hgvs": [ "NM_130444.2:c.5087G>A" ], "proteinEffect": { "hgvs": "NP_569711.2:p.Arg1696His", "hgvsWellDefined": "NP_569711.2:p.Arg1696His" }, "referenceSequence": "http://reg.genome.network/refseq/RS040368" }, { "coordinates": [ { "allele": "A", "end": 3936, "referenceAllele": "G", "start": 3935 } ], "gene": "http://reg.genome.network/gene/GN002195", "geneNCBI_id": 80781, "geneSymbol": "COL18A1", "hgvs": [ "NM_130445.3:c.3842G>A" ], "proteinEffect": { "hgvs": "NP_569712.2:p.Arg1281His", "hgvsWellDefined": "NP_569712.2:p.Arg1281His" }, "referenceSequence": "http://reg.genome.network/refseq/RS040369" }, { "coordinates": [ { "allele": "T", "end": 2104, "endIntronDirection": "-", "endIntronOffset": 9259, "referenceAllele": "C", "start": 2104, "startIntronDirection": "-", "startIntronOffset": 9260 } ], "gene": "http://reg.genome.network/gene/GN010937", "geneNCBI_id": 6573, "geneSymbol": "SLC19A1", "hgvs": [ "XM_011529707.1:c.1585-9260C>T" ], "proteinEffect": { "hgvs": "XP_011528009.1:n.1585-9260C>T" }, "referenceSequence": "http://reg.genome.network/refseq/RS096773" }, { "coordinates": [ { "allele": "T", "end": 2285, "endIntronDirection": "-", "endIntronOffset": 9259, "referenceAllele": "C", "start": 2285, "startIntronDirection": "-", "startIntronOffset": 9260 } ], "gene": "http://reg.genome.network/gene/GN010937", "geneNCBI_id": 6573, "geneSymbol": "SLC19A1", "hgvs": [ "XM_017028445.2:c.1585-9260C>T" ], "proteinEffect": { "hgvs": "XP_016883934.1:n.1585-9260C>T" }, "referenceSequence": "http://reg.genome.network/refseq/RS578196" }, { "@id": "http://reg.genome.network/allele/PA2830036660", "coordinates": [ { "allele": "A", "end": 4391, "referenceAllele": "G", "start": 4390 } ], "gene": "http://reg.genome.network/gene/GN002195", "geneNCBI_id": 80781, "geneSymbol": "COL18A1", "hgvs": [ "NM_030582.4:c.4382G>A" ], "proteinEffect": { "hgvs": "NP_085059.2:p.Arg1461His", "hgvsWellDefined": "NP_085059.2:p.Arg1461His" }, "referenceSequence": "http://reg.genome.network/refseq/RS670969" }, { "@id": "http://reg.genome.network/allele/PA2573296684", "coordinates": [ { "allele": "A", "end": 5096, "referenceAllele": "G", "start": 5095 } ], "gene": "http://reg.genome.network/gene/GN002195", "geneNCBI_id": 80781, "geneSymbol": "COL18A1", "hgvs": [ "NM_130444.3:c.5087G>A" ], "proteinEffect": { "hgvs": "NP_569711.2:p.Arg1696His", "hgvsWellDefined": "NP_569711.2:p.Arg1696His" }, "referenceSequence": "http://reg.genome.network/refseq/RS671793" }, { "coordinates": [ { "allele": "A", "end": 3908, "referenceAllele": "G", "start": 3907 } ], "gene": "http://reg.genome.network/gene/GN002195", "geneNCBI_id": 80781, "geneSymbol": "COL18A1", "hgvs": [ "NM_130445.4:c.3842G>A" ], "proteinEffect": { "hgvs": "NP_569712.2:p.Arg1281His", "hgvsWellDefined": "NP_569712.2:p.Arg1281His" }, "referenceSequence": "http://reg.genome.network/refseq/RS671794" }, { "@id": "http://reg.genome.network/allele/PA2828834226", "coordinates": [ { "allele": "A", "end": 3917, "referenceAllele": "G", "start": 3916 } ], "gene": "http://reg.genome.network/gene/GN002195", "geneNCBI_id": 80781, "geneSymbol": "COL18A1", "hgvs": [ "NM_001379500.1:c.3851G>A" ], "proteinEffect": { "hgvs": "NP_001366429.1:p.Arg1284His", "hgvsWellDefined": "NP_001366429.1:p.Arg1284His" }, "referenceSequence": "http://reg.genome.network/refseq/RS722006", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000651438.1:c.3851G>A" }, "RefSeq": { "hgvs": "NM_001379500.1:c.3851G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000498485.1:p.Arg1284His" }, "RefSeq": { "hgvs": "NP_001366429.1:p.Arg1284His" } } } } ], "type": "nucleotide" }