ClinVar Miner

Submissions for variant NM_001378454.1(ALMS1):c.451-5T>G

gnomAD frequency: 0.00004  dbSNP: rs774098604
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000634822 SCV000756166 likely benign Alstrom syndrome 2024-01-18 criteria provided, single submitter clinical testing
Counsyl RCV000634822 SCV000797915 uncertain significance Alstrom syndrome 2018-02-14 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001193872 SCV001363030 likely benign not specified 2023-05-15 criteria provided, single submitter clinical testing Variant summary: ALMS1 c.451-5T>G (also known as c.454-5T>G) alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Two predict the variant abolishes a canonical 3' acceptor site and two predict the variant weakens the same canonical 3' acceptor site. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.00014 in 248930 control chromosomes (gnomAD), predominantly at a frequency of 0.0019 within the East Asian subpopulation in the gnomAD database. The observed variant frequency within East Asian control individuals in the gnomAD database is approximately 1.3 fold of the estimated maximal expected allele frequency for a pathogenic variant in ALMS1 causing Alstrom Syndrome (0.0014), suggesting that the variant may be a benign polymorphism found primarily in populations of East Asian origin. c.451-5T>G has been reported in the literature in individuals affected with Alstrom Syndrome, retinitis pigmentosa and in an individual affected with combined 17 alpha hydroxylase/17,20-lyase deficiency without strong evidence of causality (Marshall_2015, Xu_2016, Zhang_2018). These reports do not provide unequivocal conclusions about association of the variant with Alstrom Syndrome. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 25846608, 26010121, 29345162). Four ClinVar submitters have assessed the variant since 2014: two have classified the variant as uncertain significance and two as likely benign. Based on the evidence outlined above, the variant was classified as likely benign.
Ambry Genetics RCV002334077 SCV002639929 likely benign Cardiovascular phenotype 2023-05-27 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Natera, Inc. RCV000634822 SCV001453433 likely benign Alstrom syndrome 2020-01-09 no assertion criteria provided clinical testing

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