ClinVar Miner

Submissions for variant NM_032119.4(ADGRV1):c.3269T>C (p.Ile1090Thr) (rs771410054)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000606863 SCV000731662 uncertain significance not specified 2017-05-18 criteria provided, single submitter clinical testing Variant classified as Uncertain Significance - Favor Benign. The p.Ile1090Thr va riant in GPR98 has not been previously reported in individuals with hearing, but has been identified in 0.2% (19/10124) of Ashkenazi Jewish chromosomes by the G enome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs77 1410054). Computational prediction tools and conservation analyses do not provid e strong support for or against an impact to the protein. In summary, while the clinical significance of the p.Ile1090Thr variant is uncertain, its frequency in the general population suggests that it is more likely to be benign.
Illumina Clinical Services Laboratory,Illumina RCV001151215 SCV001312327 uncertain significance Usher syndrome, type 2C 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Ambry Genetics RCV001267530 SCV001445711 uncertain significance Inborn genetic diseases 2016-11-22 criteria provided, single submitter clinical testing
Invitae RCV001304754 SCV001494048 uncertain significance not provided 2020-07-03 criteria provided, single submitter clinical testing This sequence change replaces isoleucine with threonine at codon 1090 of the ADGRV1 protein (p.Ile1090Thr). The isoleucine residue is moderately conserved and there is a moderate physicochemical difference between isoleucine and threonine. This variant is present in population databases (rs771410054, ExAC 0.02%). This variant has not been reported in the literature in individuals with ADGRV1-related conditions. ClinVar contains an entry for this variant (Variation ID: 517398). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: Deleterious; PolyPhen-2: Possibly Damaging; Align-GVGD: Class C0). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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