ClinVar Miner

Submissions for variant NM_033305.3(VPS13A):c.7953+1G>A

gnomAD frequency: 0.00002  dbSNP: rs372141290
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000811112 SCV000951360 likely pathogenic not provided 2023-12-13 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 56 of the VPS13A gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in VPS13A are known to be pathogenic (PMID: 12404112, 21598378). This variant is present in population databases (rs372141290, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with VPS13A-related conditions. ClinVar contains an entry for this variant (Variation ID: 655028). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Natera, Inc. RCV001830771 SCV002081099 likely pathogenic Chorea-acanthocytosis 2020-08-18 no assertion criteria provided clinical testing

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