ClinVar Miner

Submissions for variant NM_000069.3(CACNA1S):c.3414+3A>T

gnomAD frequency: 0.00001  dbSNP: rs892742196
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV002264936 SCV000520144 uncertain significance not provided 2022-07-11 criteria provided, single submitter clinical testing See Variant Classification Assertion Criteria.
Invitae RCV000529294 SCV000653691 pathogenic Hypokalemic periodic paralysis, type 1; Malignant hyperthermia, susceptibility to, 5 2023-08-23 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. 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 may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 381082). This variant has been observed in individuals with clinical features of autosomal recessive congenital myopathy (Invitae). It has also been observed to segregate with disease in related individuals. This variant is present in population databases (no rsID available, gnomAD 0.003%). This sequence change falls in intron 26 of the CACNA1S gene. It does not directly change the encoded amino acid sequence of the CACNA1S protein. It affects a nucleotide within the consensus splice site.
PreventionGenetics, part of Exact Sciences RCV003897864 SCV004709877 uncertain significance CACNA1S-related condition 2023-11-15 criteria provided, single submitter clinical testing The CACNA1S c.3414+3A>T variant is predicted to interfere with splicing. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0056% of alleles in individuals of Latino descent in gnomAD (http://gnomad.broadinstitute.org/variant/1-201029783-T-A). 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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