ClinVar Miner

Submissions for variant NM_000543.5(SMPD1):c.1550A>T (p.Glu517Val) (rs142787001)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000179328 SCV000605228 uncertain significance not specified 2017-02-02 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000179328 SCV000231560 likely benign not specified 2017-01-06 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000179328 SCV000920238 uncertain significance not specified 2017-11-07 criteria provided, single submitter clinical testing Variant summary: The SMPD1 c.1550A>T (p.Glu517Val) variant involves the alteration of a conserved nucleotide. 3/4 in silico tools predict a damaging outcome for this variant (SNPsandGO not captured due to low reliability index). This variant was found in 682/277056 control chromosomes, predominantly observed in the European (Non-Finnish) subpopulation at a frequency of 0.004085 (517/126550). This frequency is about 2 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 European (Non-Finnish) origin. It has been reported in multiple affected individuals without strong evidence for causality. In addition, multiple clinical diagnostic laboratories/reputable databases classified this likely benign or variant as uncertain significance. Taken together, this variant is classified as VUS-possibly benign.

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