ClinVar Miner

Submissions for variant NM_152594.3(SPRED1):c.926T>C (p.Val309Ala) (rs114636635)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000154849 SCV000204531 likely benign not specified 2012-03-19 criteria provided, single submitter clinical testing p.Val309Ala in Exon 07 of SPRED1: This variant is not expected to have clinical significance because it has been identified in 0.6% (21/3738) of African America n chromosomes from a broad population by the NHLBI Exome Sequencing Project (htt p://evs.gs.washington.edu/EVS; dbSNP rs114636635).
Invitae RCV000456632 SCV000560562 benign Legius syndrome 2019-12-31 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000586323 SCV000699951 benign not provided 2017-04-17 criteria provided, single submitter clinical testing Variant summary: The SPRED1 c.926T>C (p.Val309Ala) variant involves the alteration of a conserved nucleotide and is predicted to be benign by 3/5 in silico tools. This variant was found in 81/121216 control chromosomes from ExAC at a frequency of 0.0006682, which is approximately 267 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 likely benign/benign and it is also classified as likely benign in a publication with an indication of benign functional outcome (Brems_2012). Taken together, this variant is classified as benign.
GeneDx RCV000154849 SCV000730787 likely benign not specified 2018-02-21 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.
Center for Human Genetics, Inc,Center for Human Genetics, Inc RCV000456632 SCV000782327 uncertain significance Legius syndrome 2016-11-01 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000456632 SCV001274827 benign Legius syndrome 2017-10-15 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.
Clinical Molecular Genetics Laboratory,Johns Hopkins All Children's Hospital RCV000456632 SCV000692375 uncertain significance Legius syndrome 2014-12-08 no assertion criteria provided clinical testing

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