ClinVar Miner

Submissions for variant NM_152594.3(SPRED1):c.291G>A (p.Lys97=) (rs7182445)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000041241 SCV000058320 benign not specified 2015-09-10 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000041241 SCV000064932 benign not specified 2012-03-14 criteria provided, single submitter clinical testing Lys97Lys in exon 3 of SPRED1: This variant is not expected to have clinical sign ificance because it does not alter an amino acid residue, is not located within the splice consensus sequence, and it has been identified in 90% (6302/7020) of European American chromosomes and 69% (2576/3738) of African American chromosome s from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.w ashington.edu/EVS/; dbSNP rs7182445).
PreventionGenetics,PreventionGenetics RCV000041241 SCV000316209 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000034273 SCV000390787 benign Legius syndrome 2018-01-12 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.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000034273 SCV000605256 benign Legius syndrome 2018-07-03 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000588250 SCV000699958 benign not provided 2017-04-17 criteria provided, single submitter clinical testing Variant summary: The SPRED1 c.291G>A (p.Lys97Lys) variant involves the alteration of a conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a polymorphism outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts loss of the SRp40 and SF2/ASF binding motifs. However, these predictions have yet to be confirmed by functional studies. The variant of interest has been found in a large, broad control population, ExAC in 104831/121368 control chromosomes (45684 homozygotes) at a frequency of 0.863745, which is approximately 345498 times the estimated maximal expected allele frequency of a pathogenic SPRED1 variant (0.0000025), suggesting this variant is likely a benign polymorphism. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications; nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as benign.
Invitae RCV000034273 SCV001000160 benign Legius syndrome 2019-12-31 criteria provided, single submitter clinical testing
GeneReviews RCV000034273 SCV000058213 benign Legius syndrome 2010-10-14 no assertion criteria provided curation Converted during submission to Benign.
Diagnostic Laboratory, Department of Genetics,University Medical Center Groningen RCV000034273 SCV000733436 benign Legius syndrome no assertion criteria provided clinical testing

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