ClinVar Miner

Submissions for variant NM_001378454.1(ALMS1):c.9782-19C>A

gnomAD frequency: 0.00004  dbSNP: rs777706370
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000612132 SCV000721981 likely benign not specified 2017-08-11 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000612132 SCV001431878 uncertain significance not specified 2021-05-24 criteria provided, single submitter clinical testing Variant summary: ALMS1 c.9779-19C>A (also known as c.9785-19C>A in RefSeq) alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 4/4 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 7.6e-05 in 249140 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in ALMS1 causing Alstrom Syndrome With Dilated Cardiomyopathy (7.6e-05 vs 0.0018), allowing no conclusion about variant significance. To our knowledge, no occurrence of c.9779-19C>A in individuals affected with Alstrom Syndrome With Dilated Cardiomyopathy and no experimental evidence demonstrating its impact on protein function have been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified the variant as likely benign. Based on the evidence outlined above, the variant was classified as VUS-possibly benign.
Labcorp Genetics (formerly Invitae), Labcorp RCV002064006 SCV002467900 likely benign Alstrom syndrome 2023-12-13 criteria provided, single submitter clinical testing

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