ClinVar Miner

Submissions for variant NM_152594.3(SPRED1):c.583-7A>G (rs115970207)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000041244 SCV000064935 benign not specified 2012-03-19 criteria provided, single submitter clinical testing c.583-7A>G in Intron 05 of SPRED1: This variant is not expected to have clinical significance because it has been identified in 2.4% (88/3738) of African Americ an chromosomes from a broad population by the NHLBI Exome Sequencing Project (ht tp://evs.gs.washington.edu/EVS; dbSNP rs115970207).
Invitae RCV000206311 SCV000260565 benign Legius syndrome 2019-12-31 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000041244 SCV000316212 likely benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000206311 SCV000390791 benign Legius syndrome 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.
Integrated Genetics/Laboratory Corporation of America RCV000590597 SCV000699962 benign not provided 2017-04-17 criteria provided, single submitter clinical testing Variant summary: The SPRED1 c.583-7A>G variant involves the alteration of a non-conserved intronic nucleotide. 5/5 splice prediction tools predict no significant impact on normal splicing. This variant was found in 248/117724 control chromosomes (including 4 homozygotes) from ExAC, predominantly observed in the African subpopulation at a frequency of 0.022615 (229/10126). This frequency is about 9046 times the estimated maximal expected allele frequency of a pathogenic SPRED1 variant (0.0000025), therefore this is likely a benign polymorphism found primarily in the populations of African origin. In addition, multiple clinical diagnostic laboratories/reputable databases have classified this variant as benign/likely benign. Taken together, this variant is classified as Benign.
GeneDx RCV000041244 SCV000729623 benign not specified 2017-02-02 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.

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