ClinVar Miner

Submissions for variant NM_000543.5(SMPD1):c.107T>C (p.Val36Ala)

gnomAD frequency: 0.44445  dbSNP: rs1050228
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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000079189 SCV000111058 benign not specified 2018-02-01 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003891542 SCV000305089 benign SMPD1-related disorder 2020-02-07 criteria provided, single submitter clinical testing This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
Illumina Laboratory Services, Illumina RCV000315171 SCV000372921 benign Niemann-Pick disease, type A 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV000079189 SCV000540391 benign not specified 2016-03-28 criteria provided, single submitter clinical testing Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: MAF
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000587397 SCV000697410 benign not provided 2016-09-05 criteria provided, single submitter clinical testing Variant Summary: The c.107T>C in SMPD1 gene is a missense change that involves the alteration of a non-conserved nucleotide and 4/5 in silico tools predict benign outcome. The variant was observed in the large and broad cohorts of the ExAC project at an allele frequency of 0.6 (61590/110368 chrs tested). This frequency exceeds the maximal expected allele frequency for a pathogenic variant in this gene (0.002). A reputable database/diagnostic center has classified the variant of interest as Benign. Taking together, based on the prevalence in general population, the variant was classified as Benign.
Invitae RCV001520553 SCV001729675 benign Niemann-Pick disease, type B; Niemann-Pick disease, type A 2024-02-01 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000315171 SCV001749169 benign Niemann-Pick disease, type A 2021-07-01 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001533318 SCV001749170 benign Niemann-Pick disease, type B 2021-07-01 criteria provided, single submitter clinical testing
GeneDx RCV000587397 SCV001943942 benign not provided 2018-12-04 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 25811928, 26084044, 30795770)
Mayo Clinic Laboratories, Mayo Clinic RCV000587397 SCV000801054 benign not provided 2015-10-22 no assertion criteria provided clinical testing
Natera, Inc. RCV000315171 SCV002091664 benign Niemann-Pick disease, type A 2017-05-06 no assertion criteria provided clinical testing

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