Submissions for variant NM_000543.5(SMPD1):c.107_118del (p.Val36_Leu39del)

dbSNP: rs550365194

Total submissions: 11

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Eurofins Ntd Llc (ga)	RCV000173156	SCV000224248	benign	not specified	2015-01-22	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV000173156	SCV000305087	benign	not specified	2016-03-24	criteria provided, single submitter	clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000590646	SCV000605227	benign	not provided	2023-11-29	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000173156	SCV000697409	benign	not specified	2021-12-20	criteria provided, single submitter	clinical testing	Variant summary: SMPD1 c.107_118del12 (p.Val36_Leu39del) results in an in-frame deletion that is predicted to remove four amino acids from the encoded protein. The variant allele was found at a frequency of 0.07 in 232506 control chromosomes in the gnomAD database, including 641 homozygotes. The observed variant frequency is approximately 31.45 fold of the estimated maximal expected allele frequency for a pathogenic variant in SMPD1 causing Niemann-Pick Disease Type A phenotype (0.0022), strongly suggesting that the variant is benign. Six 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.
GeneDx	RCV000590646	SCV000970320	benign	not provided	2018-06-01	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.
Labcorp Genetics (formerly Invitae), Labcorp	RCV001514585	SCV001722463	benign	Niemann-Pick disease, type B; Niemann-Pick disease, type A	2024-02-01	criteria provided, single submitter	clinical testing
Mayo Clinic Laboratories, Mayo Clinic	RCV000590646	SCV000801053	benign	not provided	2017-05-02	no assertion criteria provided	clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV000173156	SCV001744890	benign	not specified		no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV000173156	SCV001929739	benign	not specified		no assertion criteria provided	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000173156	SCV001975155	benign	not specified		no assertion criteria provided	clinical testing
Natera, Inc.	RCV001831993	SCV002091657	benign	Niemann-Pick disease, type A	2017-05-06	no assertion criteria provided	clinical testing