ClinVar Miner

Submissions for variant NM_000543.5(SMPD1):c.107_124del (p.Val36_Leu41del)

dbSNP: rs794726889
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000173157 SCV000224249 benign not specified 2015-02-13 criteria provided, single submitter clinical testing
Invitae RCV000970558 SCV001118144 benign Niemann-Pick disease, type B; Niemann-Pick disease, type A 2024-01-31 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000173157 SCV001623280 benign not specified 2021-05-15 criteria provided, single submitter clinical testing Variant summary: SMPD1 c.107_124del18 (p.Val36_Leu41del) results in an in-frame deletion that is predicted to remove six amino acids from the encoded protein. The variant allele was found at a frequency of 0.0014 in 232506 control chromosomes in the gnomAD database, including 3 homozygotes. This frequency is close to that expected for a pathogenic variant in SMPD1 causing Niemann-Pick Disease Type A (0.0014 vs 0.0022), suggestive of a benign outcome. To our knowledge, no occurrence of c.107_124del18 in individuals affected with Niemann-Pick Disease Type A and no experimental evidence demonstrating its impact on protein function have been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as benign. Based on the evidence outlined above, the variant was classified as benign.
PreventionGenetics, part of Exact Sciences RCV003907548 SCV004726927 likely benign SMPD1-related disorder 2020-12-04 criteria provided, single submitter clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
Natera, Inc. RCV001826871 SCV002091656 likely benign Niemann-Pick disease, type A 2017-05-23 no assertion criteria provided clinical testing

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