ClinVar Miner

Submissions for variant NM_001378454.1(ALMS1):c.325-1G>A

dbSNP: rs764337753
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000674281 SCV000799591 likely pathogenic Alstrom syndrome 2018-04-26 criteria provided, single submitter clinical testing
Ambry Genetics RCV002442400 SCV002611491 uncertain significance Cardiovascular phenotype 2021-11-02 criteria provided, single submitter clinical testing The c.328-1G>A intronic variant results from a G to A substitution one nucleotide upstream from coding exon 2 of the ALMS1 gene. Alterations that disrupt the canonical splice site are expected to cause aberrant splicing. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site. The resulting transcript is predicted to be in-frame and is not expected to trigger nonsense-mediated mRNA decay; however, direct evidence is unavailable. The exact functional effect of the altered amino acid sequence is unknown. This nucleotide position is highly conserved in available vertebrate species. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Invitae RCV000674281 SCV004561288 likely pathogenic Alstrom syndrome 2023-08-07 criteria provided, single submitter clinical testing 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. 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: 558064). This variant has not been reported in the literature in individuals affected with ALMS1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change affects an acceptor splice site in intron 1 of the ALMS1 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 ALMS1 are known to be pathogenic (PMID: 17594715).

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