ClinVar Miner

Submissions for variant NM_015120.4(ALMS1):c.6010A>G (p.Ile2004Val) (rs7587103)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001081166 SCV000262084 benign Alstrom syndrome 2019-12-31 criteria provided, single submitter clinical testing
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000224015 SCV000281591 likely benign not provided 2015-12-22 criteria provided, single submitter clinical testing Converted during submission to Likely benign.
GeneDx RCV000419177 SCV000533283 likely benign not specified 2017-12-12 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.
Integrated Genetics/Laboratory Corporation of America RCV000419177 SCV000864112 likely benign not specified 2016-02-15 criteria provided, single submitter clinical testing Variant summary: The c.6004A>G (alternative name c.6010A>G) variant affects a non-conserved nucleotide, resulting in amino acid change from Ile to Val. 5/5 in-silico tools predict benign outcome for this variant. 3/5 programs in Alamut predict that this variant does not affect normal splicing. ESEfinder predicts that this variant may affect the binding site of SRp55. However, these predictions have not been confirmed by experimental evidence. This variant is found in 124/9766 African control chromosomes at a frequency of 0.0127, which is about 5 times of the maximal expected frequency of a pathogenic allele (0.0022361), suggesting this variant is benign. In addition, one clinical laboratory classified this variant as benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical laboratories; nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as likely benign.
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000419177 SCV000967145 likely benign not specified 2016-03-21 criteria provided, single submitter clinical testing p.Ile2002Val in exon 8 of ALMS1: This variant is not expected to have clinical s ignificance because it has been identified in 1.27% (124/9766) of African chromo somes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs7587103).
Personalized Diabetes Medicine Program,University of Maryland School of Medicine RCV001172525 SCV001335578 likely benign Monogenic diabetes 2018-03-27 criteria provided, single submitter research ACMG criteria: BP4(8 predictors, REVEL=0.017),BS1(1.27% in ExAC African population), BP1(missense in gene with truncating cause disease), 1 homozygote in gnomAD=likely benign

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