ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.6048G>A (p.Ala2016=)

gnomAD frequency: 0.00013  dbSNP: rs200691718
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001350881 SCV001545306 uncertain significance Cohen syndrome 2025-01-13 criteria provided, single submitter clinical testing This sequence change affects codon 2041 of the VPS13B mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the VPS13B protein. This variant is present in population databases (rs200691718, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with VPS13B-related conditions. ClinVar contains an entry for this variant (Variation ID: 1046333). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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.
Natera, Inc. RCV001350881 SCV002082599 uncertain significance Cohen syndrome 2020-03-20 no assertion criteria provided clinical testing
PreventionGenetics, part of Exact Sciences RCV003399143 SCV004105529 uncertain significance VPS13B-related disorder 2024-06-28 no assertion criteria provided clinical testing The VPS13B c.6048G>A variant is not predicted to result in an amino acid change (p.=). This variant is predicted to create a cryptic splice acceptor site according to an in silico splicing algorithm (SpliceAI, Jaganathan K, et al. 2019. PubMed ID: 30661751). However, such computer prediction programs are imperfect. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.011% of alleles in individuals of Latino descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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