ClinVar Miner

Submissions for variant NM_015120.4(ALMS1):c.6540C>T (p.Thr2180=) (rs371511963)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000431183 SCV000532474 likely benign not specified 2016-10-07 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.
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000730690 SCV000858448 uncertain significance not provided 2017-12-20 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000431183 SCV000864115 uncertain significance not specified 2017-03-06 criteria provided, single submitter clinical testing Variant summary: The ALMS1 c.6534C>T (alternative name c.6540C>T) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. Mutation Taster predicts a benign outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect binding of ESE sites. However, these predictions have yet to be confirmed by functional studies. This variant was found in 15/120306 control chromosomes at a frequency of 0.0001247, which does not exceed the estimated maximal expected allele frequency of a pathogenic ALMS1 variant (0.0022361). The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical diagnostic laboratories; nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as VUS-possibly benign.
Invitae RCV001084643 SCV001003203 likely benign Alstrom syndrome 2019-12-31 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000431183 SCV001365661 likely benign not specified 2017-08-23 criteria provided, single submitter clinical testing p.Thr2178Thr in exon 8 of ALMS1: This variant is not expected to have clinical significance because it does not alter an amino acid residue and is not located within the splice consensus sequence. It has been identified in 0.02% (13/66518) of European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs371511963).

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