ClinVar Miner

Submissions for variant NM_001128840.3(CACNA1D):c.3115-3C>T

gnomAD frequency: 0.00010  dbSNP: rs779910083
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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, Mass General Brigham Personalized Medicine RCV000603518 SCV000731664 uncertain significance not specified 2017-05-18 criteria provided, single submitter clinical testing The c.3175-3C>T variant in CACNA1D has not been previously reported in individua ls with hearing loss but has been identified in 9/24028 African chromosomes by t he Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs779910083). Although this variant has been seen in the general population, its frequency is not high enough to rule out a pathogenic role. This variant is loc ated in the 3' splice region. Computational tools do not suggest an impact to sp licing. However, this information is not predictive enough to rule out pathogeni city. In summary, the clinical significance of the c.3175-3C>T variant is uncert ain.
Eurofins Ntd Llc (ga) RCV000728052 SCV000855577 uncertain significance not provided 2017-07-25 criteria provided, single submitter clinical testing
GeneDx RCV000728052 SCV001982990 likely benign not provided 2021-04-07 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000728052 SCV002183431 uncertain significance not provided 2024-12-04 criteria provided, single submitter clinical testing This sequence change falls in intron 25 of the CACNA1D gene. It does not directly change the encoded amino acid sequence of the CACNA1D protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs779910083, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with CACNA1D-related conditions. ClinVar contains an entry for this variant (Variation ID: 517400). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. 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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