ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.1463C>T (p.Thr488Met)

gnomAD frequency: 0.00050  dbSNP: rs150783688
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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000488217 SCV000113814 uncertain significance not provided 2013-06-04 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000335692 SCV000470767 uncertain significance Cohen syndrome 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.
CeGaT Center for Human Genetics Tuebingen RCV000488217 SCV000575565 likely benign not provided 2023-01-01 criteria provided, single submitter clinical testing VPS13B: BP4, BS2
Genetic Services Laboratory, University of Chicago RCV000081879 SCV000597875 uncertain significance not specified 2016-02-16 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000335692 SCV000755439 likely benign Cohen syndrome 2024-02-01 criteria provided, single submitter clinical testing
Ambry Genetics RCV002514436 SCV003618431 likely benign Inborn genetic diseases 2022-01-25 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, 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.
PreventionGenetics, part of Exact Sciences RCV003915092 SCV004734724 likely benign VPS13B-related disorder 2019-07-12 criteria provided, single submitter clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
Natera, Inc. RCV000335692 SCV001454224 benign Cohen syndrome 2019-12-31 no assertion criteria provided clinical testing
Clinical Genetics, Academic Medical Center RCV000488217 SCV002034564 likely benign not provided no assertion criteria provided clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV000488217 SCV002035830 likely benign not provided no assertion criteria provided clinical testing

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