ClinVar Miner

Submissions for variant NM_001378454.1(ALMS1):c.3732G>A (p.Lys1244=)

gnomAD frequency: 0.00138  dbSNP: rs140670994
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000180330 SCV000232742 likely benign not specified 2015-03-05 criteria provided, single submitter clinical testing
GeneDx RCV001697172 SCV000534132 likely benign not provided 2021-03-29 criteria provided, single submitter clinical testing
Invitae RCV000559280 SCV000631778 likely benign Alstrom syndrome 2024-01-28 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000180330 SCV000864090 benign not specified 2016-11-28 criteria provided, single submitter clinical testing Variant summary: The c.3729G>A (alternative name c.3735G>A) in ALMS1 gene is a synonymous change that involves a non-conserved nucleotide. 5/5 programs in Alamut predict that this variant does not affect a normal splicing, however no functional studies supporting these predictions were published at the time of evaluation. The variant is present in the large control population dataset of ExAC at a frequency 0.0004 (48/120640 chrs tested), predominantly in individuals of African origin (0.0045; 44/9792 chrs tested). This frequency exceeds the estimated maximal expected allele frequency of a pathogenic variant in ALMS1 gene (0.0022). The variant is present in a control population dataset of gmomAD predominantly in individuals of African origin: 0.0045 (117/ 25854 chrs); however, since the data set is still in beta mode, this data was not captured in pbGP. The c. 3729G>A has not, to our knowledge, been reported in affected individuals via published reports, but is cited as Likely Benign by a reputable database/clinical laboratory. The variant seems to be an ethnic specific polymorphism, therefore it has been classified as Benign.
Ambry Genetics RCV002362926 SCV002624186 benign Cardiovascular phenotype 2019-02-01 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, 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.

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