ClinVar Miner

Submissions for variant NM_015120.4(ALMS1):c.9917A>G (p.Asn3306Ser) (rs142022233)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Personalized Diabetes Medicine Program,University of Maryland School of Medicine RCV000445528 SCV000536987 benign Monogenic diabetes 2016-03-18 criteria provided, single submitter research ACMG Criteria: PP3, BS1 (ExAC SAS), BS2 (ExAC SAS), BP1, BP4
Invitae RCV000532855 SCV000631813 benign not provided 2019-03-05 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000602571 SCV000711823 benign not specified 2016-03-21 criteria provided, single submitter clinical testing p.Asn3304Ser in exon 13 of ALMS1: This variant is not expected to have clinical significance because it has been identified in 2.76% (455/16484) of South Asian chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitut e.org; dbSNP rs142022233).
GeneDx RCV000602571 SCV000714608 benign not specified 2017-01-24 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 RCV000602571 SCV000864096 benign not specified 2018-01-02 criteria provided, single submitter clinical testing Variant summary: The ALMS1 c.9911A>G (p.Asn3304Ser; alternative nomenclature c.9917A>G, p.N3306S) variant involves the alteration of a conserved nucleotide. 2/3 in silico tools predict a benign outcome for this variant. This variant was found in 1363/276886 control chromosomes, predominantly observed in the South Asian subpopulation at a frequency of 0.026704 (821/30744), including 19 homozygotes. 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 South Asian origin. An internal specimen also carries a pathogenic MYBPC3, supporting the benign role of the variant. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. Taken together, this variant is classified as benign.

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