ClinVar Miner

Submissions for variant NM_001378454.1(ALMS1):c.9822C>G (p.Thr3274=) (rs201446579)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
CeGaT Praxis fuer Humangenetik Tuebingen RCV000415799 SCV000493281 likely benign not provided 2021-04-01 criteria provided, single submitter clinical testing
GeneDx RCV000415799 SCV000531880 likely benign not provided 2020-11-11 criteria provided, single submitter clinical testing
Invitae RCV001084056 SCV000631812 benign Alstrom syndrome 2020-12-05 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000443000 SCV001363236 benign not specified 2019-04-22 criteria provided, single submitter clinical testing Variant summary: ALMS1 c.9819C>G (also known as c.9825C>G) alters a non-conserved nucleotide resulting in a synonymous change. 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 0.0023 in 249364 control chromosomes, predominantly at a frequency of 0.0029 within the Non-Finnish European subpopulation in the gnomAD database. The observed variant frequency within Non-Finnish European 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 Cardiomyopathy phenotype (0.0022), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Non-Finnish European origin. To our knowledge, no occurrence of c.9819C>G in individuals affected with Cardiomyopathy and no experimental evidence demonstrating its impact on protein function have been reported. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation (2x Benign/likely benign ; 1x uncertain significance). Based on the evidence outlined above, the variant was classified as benign.
Pars Genome Lab RCV001084056 SCV001652886 likely benign Alstrom syndrome 2021-05-18 criteria provided, single submitter clinical testing
Clinical Genetics,Academic Medical Center RCV000443000 SCV001917533 benign not specified no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000415799 SCV001974156 likely benign not provided no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000415799 SCV002034150 likely benign not provided no assertion criteria provided clinical testing

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