ClinVar Miner

Submissions for variant NM_001378454.1(ALMS1):c.10272G>C (p.Lys3424Asn) (rs34398445)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001084442 SCV000290060 benign Alstrom syndrome 2019-12-31 criteria provided, single submitter clinical testing
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000434583 SCV000510877 benign not provided 2016-09-01 criteria provided, single submitter clinical testing
GeneDx RCV000438106 SCV000534464 benign not specified 2016-12-27 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.
Personalized Diabetes Medicine Program,University of Maryland School of Medicine RCV000445397 SCV000536988 benign Monogenic diabetes 2018-10-12 criteria provided, single submitter research ACMG criteria: BP1 (disease caused by truncating variants), BA1 (1.9% in gnomAD African), BS2 (6 homozygotes in gnomAD African), BP4 (7 predictors + REVEL 0.039)= benign
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000438106 SCV000711801 benign not specified 2016-03-21 criteria provided, single submitter clinical testing p.Lys3423Asn in exon 15 of ALMS1: This variant is not expected to have clinical significance because it has been identified in 3.03% (40/1322) of African chromo somes by the 1000 Genomes Project (Phase 3; dbSNP rs34398445).
Athena Diagnostics Inc RCV000434583 SCV000840766 likely benign not provided 2018-05-24 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000438106 SCV000864097 benign not specified 2017-02-06 criteria provided, single submitter clinical testing Variant summary: The ALMS1 c.10269G>C (p.Lys3423Asn, alternative name c.10275G>C) variant involves the alteration of a non-conserved nucleotide and is predicted to be benign by 3/5 in silico tools. This variant was found in 211/120598 control chromosomes (including four homozygotes), predominantly observed in the African subpopulation at a frequency of 0.019804 (194/9796). This frequency is about 9 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. It has not, to our knowledge, been reported in affected individuals in literature. One clinical diagnostic laboratory has classified this variant as benign. Taken together this variant is classified as benign variant.

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