ClinVar Miner

Submissions for variant NM_000543.5(SMPD1):c.1091+10G>A

gnomAD frequency: 0.00033  dbSNP: rs148067213
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000592728 SCV000703671 uncertain significance not provided 2018-04-04 criteria provided, single submitter clinical testing
Invitae RCV001087561 SCV000755906 likely benign Niemann-Pick disease, type B; Niemann-Pick disease, type A 2023-12-12 criteria provided, single submitter clinical testing
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard RCV001249052 SCV001422998 likely benign Sphingomyelin/cholesterol lipidosis 2020-01-22 criteria provided, single submitter curation The c.1091+10G>A variant in SMPD1 has not been previously reported in individuals with Niemann-Pick disease, but has been identified in 0.120% (30/29414) of African chromosomes, 0.005% (1/19944) of East Asian chromosomes, and 0.003% (1/35414) of Latino chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs148067213). This variant has also been reported in ClinVar (VariationID: 498584) as likely benign by Invitae and as a VUS by EGL Genetic Diagnostics. Computational prediction tools, including splice predictors, and conservation analyses suggest that this variant may not impact the protein, though this information is not predictive enough to rule out pathogenicity. In summary, although additional studies are required to fully establish its clinical significance, this variant is likely benign. ACMG/AMP Criteria applied: BS1, BP4, BP7 (Richards 2015).

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