ClinVar Miner

Submissions for variant NM_015120.4(ALMS1):c.2661A>G (p.Lys887=) (rs80133984)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000228750 SCV000290079 benign Alstrom syndrome 2019-12-31 criteria provided, single submitter clinical testing
GeneDx RCV000430379 SCV000531701 likely benign not specified 2018-02-01 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.
Integrated Genetics/Laboratory Corporation of America RCV000430379 SCV000864087 benign not specified 2018-07-30 criteria provided, single submitter clinical testing Variant summary: ALMS1 c.2655A>G (alternative c.2661A>G) alters a non-conserved nucleotide resulting in a synonymous change. The variant allele was found at a frequency of 0.00081 in 276666 control chromosomes, and was predominantly within the African subpopulation in the gnomAD database at a frequency of 0.0084, including 2 homozygotes. The observed variant frequency within African control individuals is approximately 3.8-fold above the estimated maximal expected allele frequency for a pathogenic variant in ALMS1 causing Cardiomyopathy phenotype (0.0022), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African origin. To our knowledge, no occurrence of c.2655A>G in individuals affected with Cardiomyopathy and no experimental evidence demonstrating its impact on protein function have been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, and both classified the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as benign.

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