ClinVar Miner

Submissions for variant NM_152594.3(SPRED1):c.1044T>C (p.Val348=) (rs3751526)

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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000041236 SCV000058318 benign not specified 2015-12-30 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000041236 SCV000064927 benign not specified 2012-03-14 criteria provided, single submitter clinical testing Val348Val in exon 7 of SPRED1: This variant is not expected to have clinical sig nificance 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% (2574/3738) of African American chromosom es from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs. washington.edu/EVS/; dbSNP rs3751526).
PreventionGenetics,PreventionGenetics RCV000041236 SCV000316207 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000034272 SCV000390797 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.
GeneDx RCV000041236 SCV000514743 benign not specified 2015-07-14 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.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000034272 SCV000605258 benign Legius syndrome 2018-07-03 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000589810 SCV000699956 benign not provided 2017-04-18 criteria provided, single submitter clinical testing Variant summary: The SPRED1 c.1044T>C (p.Val348Val) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. Mutation taster predicts a polymorphism outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect binding of multiple ESE sites. However, no published functional studies are available to confirm these predictions. This variant was found in 104813/121358 control chromosomes (45668 homozygotes) from ExAC at a frequency of 0.8636678; therefore it is a very common polymorphism and allele C is the major allele at this cDNA position. Several clinical diagnostic laboratories/reputable databases have classified this variant as benign. Taken together, this variant is classified as Benign.
Invitae RCV000034272 SCV001000162 benign Legius syndrome 2019-12-31 criteria provided, single submitter clinical testing
GeneReviews RCV000034272 SCV000058212 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 RCV000034272 SCV000733439 benign Legius syndrome no assertion criteria provided clinical testing

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