ClinVar Miner

Submissions for variant NM_015120.4(ALMS1):c.2664A>G (p.Val888=) (rs76266696)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001086073 SCV000290080 benign Alstrom syndrome 2019-12-31 criteria provided, single submitter clinical testing
GeneDx RCV000441805 SCV000532097 benign not specified 2016-10-10 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.
Athena Diagnostics Inc RCV000710531 SCV000840771 benign not provided 2018-05-24 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000441805 SCV000864088 benign not specified 2016-09-19 criteria provided, single submitter clinical testing Variant summary: The ALMS1 c.2658A>G (p.Val886Val, alternative name c.2664A>G) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. 5/5 splice prediction tools predict a creation of cryptic donor site. This silent variant is 100 nucleotides away from the exon-intron bounday; thus it is unlikely that the cryptic site will be used. In addition, these predictions have yet to be confirmed by functional studies. This variant was found in 310/120600 control chromosomes (3 homozygotes), predominantly observed in the African subpopulation at a frequency of 0.0278175 (272/9778). This frequency is about 12 times the estimated maximal expected allele frequency of a pathogenic ALMS1 variant (0.0022361), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. In addition, one clinical diagnostic laboratory has classified this variant as benign. Taken together, this variant is classified as a benign variant.
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000441805 SCV000967039 benign not specified 2016-03-21 criteria provided, single submitter clinical testing p.Val886Val in exon 8 of ALMS1: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, is not located withi n the splice consensus sequence, and has been identified in 2.78% (272/9778) of African chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broad institute.org; dbSNP rs76266696).

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