ClinVar Miner

Submissions for variant NM_032119.4(ADGRV1):c.1797A>T (p.Arg599Ser)

gnomAD frequency: 0.00006  dbSNP: rs200058876
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000725730 SCV000338978 uncertain significance not provided 2016-02-05 criteria provided, single submitter clinical testing
Mendelics RCV000987532 SCV001136847 uncertain significance Usher syndrome type 2C 2023-06-02 criteria provided, single submitter clinical testing
Invitae RCV000725730 SCV001421406 likely benign not provided 2024-01-04 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000146071 SCV002104020 uncertain significance not specified 2022-02-16 criteria provided, single submitter clinical testing Variant summary: ADGRV1 c.1797A>T (p.Arg599Ser) results in a non-conservative amino acid change located in the Na-Ca exchanger/integrin-beta4 domain (IPR003644) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 7.6e-05 in 248454 control chromosomes (gnomAD). This frequency is not higher than expected for a pathogenic variant in ADGRV1 causing Usher Syndrome (7.6e-05 vs 0.0054), allowing no conclusion about variant significance. c.1797A>T has been reported in the literature in an individual affected with early onset hearing loss without strong evidence for causality (example: Miyagawa_2013). This report does not provide unequivocal conclusions about association of the variant with Usher Syndrome. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as VUS (n=2) and benign (n=1). Based on the evidence outlined above, the variant was classified as uncertain significance.
Genetic Services Laboratory, University of Chicago RCV000146071 SCV000193248 likely benign not specified no assertion criteria provided clinical testing

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