ClinVar Miner

Submissions for variant NM_152594.3(SPRED1):c.675C>T (p.Ser225=) (rs144764225)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000041245 SCV000064936 benign not specified 2015-10-08 criteria provided, single submitter clinical testing p.Ser225Ser in exon 6 of SPRED1: This variant is not expected to have clinical s ignificance because it has been identified in 0.15% (23/15804) of South Asian ch romosomes and 0.13% (84/64292) of European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs144764225), does not alter an amino acid residue and is not located within the splice consensus seque nce.
Invitae RCV001086681 SCV000260336 benign Legius syndrome 2019-12-31 criteria provided, single submitter clinical testing
GeneDx RCV000586803 SCV000524538 benign not provided 2016-11-23 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 RCV000586803 SCV000699963 benign not provided 2017-04-17 criteria provided, single submitter clinical testing Variant summary: The SPRED1 c.675C>T (p.Ser225Ser) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. 5/5 splice prediction tools predict no significant impact on normal splicing. This variant was found in 124/117138 control chromosomes from ExAC at a frequency of 0.0010586, which is approximately 423 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.
Illumina Clinical Services Laboratory,Illumina RCV001086681 SCV001280218 likely benign Legius syndrome 2017-04-27 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). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

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