ClinVar Miner

Submissions for variant NM_030777.4(SLC2A10):c.1559G>A (p.Ser520Asn)

gnomAD frequency: 0.00007  dbSNP: rs573480396
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000836031 SCV000977856 likely benign not provided 2021-05-13 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001358748 SCV001554599 likely benign not specified 2023-05-30 criteria provided, single submitter clinical testing Variant summary: SLC2A10 c.1559G>A (p.Ser520Asn) results in a conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00036 in 251156 control chromosomes, predominantly at a frequency of 0.0023 within the South Asian subpopulation in the gnomAD database, including 2 homozygotes. The observed variant frequency within South Asian control individuals in the gnomAD database is higher than the estimated maximal expected allele frequency for a pathogenic variant in SLC2A10 causing Arterial Tortuosity Syndrome phenotype (0.0016), suggesting that the variant is a benign polymorphism found primarily in populations of South Asian origin. To our knowledge, no occurrence of c.1559G>A in individuals affected with Arterial Tortuosity Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as benign (n=1)/likely benign (n=3). Based on the evidence outlined above, the variant was classified as likely benign.
Invitae RCV001456321 SCV001660099 likely benign Arterial tortuosity syndrome 2024-01-12 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000836031 SCV001747318 likely benign not provided 2021-06-01 criteria provided, single submitter clinical testing
Ambry Genetics RCV002404473 SCV002704937 benign Familial thoracic aortic aneurysm and aortic dissection 2020-11-12 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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