ClinVar Miner

Submissions for variant NM_015120.4(ALMS1):c.3735G>A (p.Lys1245=) (rs140670994)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000180330 SCV000232742 likely benign not specified 2015-03-05 criteria provided, single submitter clinical testing
GeneDx RCV000180330 SCV000534132 likely benign not specified 2018-02-26 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.
Invitae RCV000559280 SCV000631778 likely benign Alstrom syndrome 2019-12-31 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America 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.

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