{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA031689", "communityStandardTitle": [ "NM_020975.6(RET):c.1124T>A (p.Leu375Gln)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=221955[alleleid]", "alleleId": 221955, "preferredName": "NM_020975.6(RET):c.1124T>A (p.Leu375Gln)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/220574", "RCV": [ "RCV000591528", "RCV001083800", "RCV001532950", "RCV004530231", "RCV000564599", "RCV001294030" ], "variationId": 220574 } ], "ExAC": [ { "@id": "http://exac.broadinstitute.org/variant/10-43604539-T-A", "id": "10-43604539-T-A", "variant": "10:43604539 T / A" } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr10:g.43604539T>A?assembly=hg19", "id": "chr10:g.43604539T>A" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr10:g.43109091T>A?assembly=hg38", "id": "chr10:g.43109091T>A" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/142338976", "rs": 142338976 } ], "gnomAD_2": [ { "@id": "http://gnomad.broadinstitute.org/variant/10-43604539-T-A?dataset=gnomad_r2_1", "id": "10-43604539-T-A", "variant": "10:43604539 T / A" } ], "gnomAD_3": [ { "@id": "http://gnomad.broadinstitute.org/variant/10-43109091-T-A?dataset=gnomad_r3", "id": "10-43109091-T-A", "variant": "10:43109091 T / A" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/10-43109091-T-A?dataset=gnomad_r4", "id": "10-43109091-T-A", "variant": "10:43109091 T / A" } ] }, "genomicAlleles": [ { "chromosome": "10", "coordinates": [ { "allele": "A", "end": 43109091, "referenceAllele": "T", "start": 43109090 } ], "hgvs": [ "NC_000010.11:g.43109091T>A", "CM000672.2:g.43109091T>A" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000058" }, { "chromosome": "10", "coordinates": [ { "allele": "A", "end": 43604539, "referenceAllele": "T", "start": 43604538 } ], "hgvs": [ "NC_000010.10:g.43604539T>A", "CM000672.1:g.43604539T>A" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000034" }, { "chromosome": "10", "coordinates": [ { "allele": "A", "end": 42924545, "referenceAllele": "T", "start": 42924544 } ], "hgvs": [ "NC_000010.9:g.42924545T>A" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000010" }, { "coordinates": [ { "allele": "A", "end": 37023, "referenceAllele": "T", "start": 37022 } ], "hgvs": [ "NG_007489.1:g.37023T>A", "LRG_518:g.37023T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS000611" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 1040, "endIntronDirection": "-", "endIntronOffset": 2115, "referenceAllele": "T", "start": 1040, "startIntronDirection": "-", "startIntronOffset": 2116 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "ENST00000615310.5:c.868-2116T>A" ], "proteinEffect": { "hgvs": "ENSP00000480088.2:n.868-2116T>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS826472" }, { "coordinates": [ { "allele": "A", "end": 698, "referenceAllele": "T", "start": 697 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "ENST00000683007.1:n.698T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS827994" }, { "coordinates": [ { "allele": "A", "end": 1314, "referenceAllele": "T", "start": 1313 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "ENST00000340058.6:c.1124T>A" ], "proteinEffect": { "hgvs": "ENSP00000344798.4:p.Leu375Gln", "hgvsWellDefined": "ENSP00000344798.4:p.Leu375Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS747868" }, { "coordinates": [ { "allele": "A", "end": 1314, "referenceAllele": "T", "start": 1313 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "ENST00000355710.8:c.1124T>A" ], "proteinEffect": { "hgvs": "ENSP00000347942.3:p.Leu375Gln", "hgvsWellDefined": "ENSP00000347942.3:p.Leu375Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS748710", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000355710.8:c.1124T>A" }, "RefSeq": { "hgvs": "NM_020975.6:c.1124T>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000347942.3:p.Leu375Gln" }, "RefSeq": { "hgvs": "NP_066124.1:p.Leu375Gln" } } } }, { "coordinates": [ { "allele": "A", "end": 820, "endIntronDirection": "-", "endIntronOffset": 2115, "referenceAllele": "T", "start": 820, "startIntronDirection": "-", "startIntronOffset": 2116 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "ENST00000671844.1:c.626-2116T>A" ], "proteinEffect": { "hgvs": "ENSP00000500541.1:n.626-2116T>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS773184" }, { "coordinates": [ { "allele": "A", "end": 263, "endIntronDirection": "-", "endIntronOffset": 2115, "referenceAllele": "T", "start": 263, "startIntronDirection": "-", "startIntronOffset": 2116 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "ENST00000672389.1:c.74-2116T>A" ], "proteinEffect": { "hgvs": "ENSP00000500252.1:n.74-2116T>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS773367" }, { "coordinates": [ { "allele": "A", "end": 1304, "referenceAllele": "T", "start": 1303 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "ENST00000340058.5:c.1124T>A" ], "proteinEffect": { "hgvs": "ENSP00000344798.4:p.Leu375Gln", "hgvsWellDefined": "ENSP00000344798.4:p.Leu375Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS247408" }, { "coordinates": [ { "allele": "A", "end": 1356, "referenceAllele": "T", "start": 1355 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "ENST00000355710.7:c.1124T>A" ], "proteinEffect": { "hgvs": "ENSP00000347942.3:p.Leu375Gln", "hgvsWellDefined": "ENSP00000347942.3:p.Leu375Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS247251" }, { "coordinates": [ { "allele": "A", "end": 258, "endIntronDirection": "-", "endIntronOffset": 3007, "referenceAllele": "T", "start": 258, "startIntronDirection": "-", "startIntronOffset": 3008 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "ENST00000498820.5:c.74-3008T>A" ], "proteinEffect": { "hgvs": "ENSP00000419080.1:n.74-3008T>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS247185" }, { "coordinates": [ { "allele": "A", "end": 1314, "referenceAllele": "T", "start": 1313 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "ENST00000615310.4:c.1124T>A" ], "proteinEffect": { "hgvs": "ENSP00000480088.1:p.Leu375Gln", "hgvsWellDefined": "ENSP00000480088.1:p.Leu375Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS402558" }, { "@id": "http://reg.genome.network/allele/PA349564", "coordinates": [ { "allele": "A", "end": 1314, "referenceAllele": "T", "start": 1313 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "NM_020630.4:c.1124T>A", "LRG_518t2:c.1124T>A" ], "proteinEffect": { "hgvs": "NP_065681.1:p.Leu375Gln", "hgvsWellDefined": "NP_065681.1:p.Leu375Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS036456" }, { "@id": "http://reg.genome.network/allele/PA356795", "coordinates": [ { "allele": "A", "end": 1314, "referenceAllele": "T", "start": 1313 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "NM_020975.4:c.1124T>A", "LRG_518t1:c.1124T>A" ], "proteinEffect": { "hgvs": "NP_066124.1:p.Leu375Gln", "hgvsWellDefined": "NP_066124.1:p.Leu375Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS036733" }, { "coordinates": [ { "allele": "A", "end": 1356, "referenceAllele": "T", "start": 1355 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "XM_011540027.1:c.1124T>A" ], "proteinEffect": { "hgvs": "XP_011538329.1:p.Leu375Gln", "hgvsWellDefined": "XP_011538329.1:p.Leu375Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS106977" }, { "@id": "http://reg.genome.network/allele/PA2828046370", "coordinates": [ { "allele": "A", "end": 719, "referenceAllele": "T", "start": 718 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "NM_001355216.1:c.362T>A" ], "proteinEffect": { "hgvs": "NP_001342145.1:p.Leu121Gln", "hgvsWellDefined": "NP_001342145.1:p.Leu121Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS522845" }, { "@id": "http://reg.genome.network/allele/PA349564", "coordinates": [ { "allele": "A", "end": 1356, "referenceAllele": "T", "start": 1355 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "NM_020630.5:c.1124T>A" ], "proteinEffect": { "hgvs": "NP_065681.1:p.Leu375Gln", "hgvsWellDefined": "NP_065681.1:p.Leu375Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS525983" }, { "@id": "http://reg.genome.network/allele/PA356795", "coordinates": [ { "allele": "A", "end": 1356, "referenceAllele": "T", "start": 1355 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "NM_020975.5:c.1124T>A" ], "proteinEffect": { "hgvs": "NP_066124.1:p.Leu375Gln", "hgvsWellDefined": "NP_066124.1:p.Leu375Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS526025" }, { "@id": "http://reg.genome.network/allele/PA356795", "coordinates": [ { "allele": "A", "end": 1314, "referenceAllele": "T", "start": 1313 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "NM_020975.6:c.1124T>A" ], "proteinEffect": { "hgvs": "NP_066124.1:p.Leu375Gln", "hgvsWellDefined": "NP_066124.1:p.Leu375Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS670171", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000355710.8:c.1124T>A" }, "RefSeq": { "hgvs": "NM_020975.6:c.1124T>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000347942.3:p.Leu375Gln" }, "RefSeq": { "hgvs": "NP_066124.1:p.Leu375Gln" } } } }, { "@id": "http://reg.genome.network/allele/PA349564", "coordinates": [ { "allele": "A", "end": 1314, "referenceAllele": "T", "start": 1313 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "NM_020630.6:c.1124T>A" ], "proteinEffect": { "hgvs": "NP_065681.1:p.Leu375Gln", "hgvsWellDefined": "NP_065681.1:p.Leu375Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS728447" } ], "type": "nucleotide" }