ClinVar Miner

Submissions for variant NM_001378454.1(ALMS1):c.10628C>G (p.Thr3543Ser) (rs45501594)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001079318 SCV000262122 benign Alstrom syndrome 2019-12-31 criteria provided, single submitter clinical testing
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000224685 SCV000280969 likely benign not provided 2015-09-29 criteria provided, single submitter clinical testing Converted during submission to Likely benign.
GeneDx RCV000434829 SCV000531893 likely benign not specified 2018-01-16 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 RCV000445553 SCV000536990 benign Monogenic diabetes 2019-02-01 criteria provided, single submitter research ACMG criteria: BP4 (six predictors plus Revel score: 0.024; not using PP3's three predictors), BA1 (1% in gnomAD European population), BS2 (15 homozygotes in gnomAD), BP1 (missense variant when mostly truncating mutations)= benign
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000434829 SCV000705014 benign not specified 2017-01-25 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000434829 SCV000711946 benign not specified 2017-12-14 criteria provided, single submitter clinical testing p.Thr3542Ser in exon 16 of ALMS1: This variant is not expected to have clinical significance because it has been identified in 1.03% (1297/125086) of European c hromosomes including 12 homozygotes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org/; dbSNP rs45501594).
Athena Diagnostics Inc RCV000224685 SCV000840768 benign not provided 2018-07-31 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000434829 SCV000864099 benign not specified 2016-08-02 criteria provided, single submitter clinical testing Variant summary: The ALMS1 c.10625C>G (p.Thr3542Ser, alternative name c.10631C>G) variant involves the alteration of a non-conserved nucleotide. 4/5 in silico tools predict a benign outcome for this variant. This variant was found in 824/119494 control chromosomes (5 homozygotes), predominantly observed in the European (Non-Finnish) subpopulation at a frequency of 0.0099462 (658/66156). This frequency is about 4 to 7 times the estimated maximal expected allele frequency of a pathogenic ALMS1 variant (0.0022361) for CYMO or Alstrom Syndrom, respectively. The allele frequency in the European (Non-Finnish) subpopulation suggests that this variant is likely a benign polymorphism found primarily in the populations of European (Non-Finnish) origin. The variant has been reported in patients with clinical features of Alstrom Syndrome, but without evidence of causality (ie co-segregation or functional studies). 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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