ClinVar Miner

Submissions for variant NM_152594.3(SPRED1):c.424-18G>A (rs7179118)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000034340 SCV000058321 benign not specified 2015-09-10 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000034340 SCV000316210 benign not specified criteria provided, single submitter clinical testing
GeneDx RCV000034340 SCV000514741 benign not specified 2015-10-15 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.
Integrated Genetics/Laboratory Corporation of America RCV000589850 SCV000699959 benign not provided 2017-04-17 criteria provided, single submitter clinical testing Variant summary: The SPRED1 c.424-18G>A variant involves the alteration of a non-conserved intronic nucleotide. One in silico tool predicts a benign outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing and ESE finder predicts no impact on ESE sites at the locus. However, these predictions have yet to be confirmed by functional studies. This variant was found in the large control database ExAC at a frequency of 0.2265353 (27452/121182 control chromosomes [3368 homozygotes]), which is approximately 90614 times the estimated maximal expected allele frequency of a pathogenic SPRED1 variant (0.0000025), providing very strong evidence that this variant is likely a benign polymorphism. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. To our knowledge, the variant of interest has not been reported in affected individuals via publications, nor has it been evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as benign.
DNA and Cytogenetics Diagnostics Unit,Erasmus Medical Center RCV000616779 SCV000745401 benign Legius syndrome 2015-09-21 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000616779 SCV001157254 benign Legius syndrome 2018-11-06 criteria provided, single submitter clinical testing
Diagnostic Laboratory, Department of Genetics,University Medical Center Groningen RCV000616779 SCV000733437 benign Legius syndrome no assertion criteria provided clinical testing

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