ClinVar Miner

Submissions for variant NM_152594.3(SPRED1):c.939G>A (p.Thr313=) (rs140644874)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001079971 SCV000291526 benign Legius syndrome 2019-12-31 criteria provided, single submitter clinical testing
GeneDx RCV000588514 SCV000520807 likely benign not provided 2018-07-20 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 RCV000588514 SCV000699964 benign not provided 2017-04-18 criteria provided, single submitter clinical testing Variant summary: The SPRED1 c.939G>A (p.Thr313Thr) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant. 4/5 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 functional studies are available to confirm these predictions. This variant was found in 78/121206 control chromosomes from ExAC at a frequency of 0.0006435, which is approximately 257 times the estimated maximal expected allele frequency of a pathogenic SPRED1 variant (0.0000025), therefore this variant is likely a benign polymorphism. In addition, multiple clinical diagnostic laboratories/reputable databases have classified this variant as benign. Taken together, this variant is classified as Benign.
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000434497 SCV000710934 benign not specified 2017-11-14 criteria provided, single submitter clinical testing p.Thr313Thr in exon 7 of SPRED1: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue, is not located with in the splice consensus sequence, and has been identified in 0.1% (35/25780) of African American chromosomes by the Genome Aggregation Database (gnomAD, http:// gnomad.broadinstitute.org; dbSNP rs140644874).
Illumina Clinical Services Laboratory,Illumina RCV001079971 SCV001274828 likely 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.

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