ClinVar Miner

Submissions for variant NM_000543.5(SMPD1):c.559C>T (p.Pro187Ser)

gnomAD frequency: 0.01580  dbSNP: rs74053349
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000175625 SCV000227149 benign not specified 2015-01-27 criteria provided, single submitter clinical testing
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics RCV000224923 SCV000281231 benign not provided 2015-07-08 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000262282 SCV000372926 benign Niemann-Pick disease, type A 2018-01-13 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000175625 SCV000920240 benign not specified 2017-11-07 criteria provided, single submitter clinical testing Variant summary: The SMPD1 c.559C>T (p.Pro187Ser) variant involves the alteration of a non-conserved nucleotide and 2/3 in silico tools predict a benign outcome for this variant (SNPsandGO and Mutation Taster not captured due to low reliability index and p-value, respectively). This variant was found in 968/157662 (16 homozygotes) control chromosomes (gnomAD), predominantly observed in the African subpopulation at a frequency of 0.057086 (804/14084, 16 homozygotes)). This frequency is about 26 times the estimated maximal expected allele frequency of a pathogenic SMPD1 variant (0.0022361), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. The variant of interest has not, to our knowledge, been reported in affected individuals via publications nor was it evaluated for functional impact by in vivo/vitro studies. However, multiple clinical diagnostic laboratories/reputable databases classified this variant as "benign". Taken together, this variant is classified as Benign.
Labcorp Genetics (formerly Invitae), Labcorp RCV001081805 SCV001106835 benign Niemann-Pick disease, type B; Niemann-Pick disease, type A 2024-01-31 criteria provided, single submitter clinical testing
GeneDx RCV000224923 SCV001941538 benign not provided 2018-08-31 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV000224923 SCV005323424 benign not provided criteria provided, single submitter not provided
Natera, Inc. RCV000262282 SCV002091686 benign Niemann-Pick disease, type A 2017-06-14 no assertion criteria provided clinical testing

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