ClinVar Miner

Submissions for variant NM_001378454.1(ALMS1):c.9907+20C>T (rs74730457)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000425138 SCV000529302 benign not specified 2016-10-12 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000425138 SCV001363242 benign not specified 2019-10-29 criteria provided, single submitter clinical testing Variant summary: ALMS1 c.9904+20C>T (also known as c.9910+20C>T)alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 5/5 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 0.0068 in 280282 control chromosomes, predominantly at a frequency of 0.066 within the African or African-American subpopulation in the gnomAD database, including 59 homozygotes. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 30 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. To our knowledge, no occurrence of c.9904+20C>T in individuals affected with Cardiomyopathy and no experimental evidence demonstrating its impact on protein function have been reported. A ClinVar submission (evaluation after 2014) cites the variant as benign. Based on the evidence outlined above, the variant was classified as benign.
Invitae RCV001518925 SCV001727704 benign Alstrom syndrome 2020-11-27 criteria provided, single submitter clinical testing

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