ClinVar Miner

Submissions for variant NM_030662.4(MAP2K2):c.1093-6T>C (rs369681843)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen RASopathy Variant Curation Expert Panel RCV000463260 SCV000616563 benign Rasopathy 2017-05-09 reviewed by expert panel curation The filtering allele frequency of the c.1093-6T>C variant in the MAP2K2 gene is 0.166% (9/2834) of African chromosomes by the Exome Aggregation Consortium, which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen RASopathy Expert Panel (BA1; PMID:29493581)
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000039471 SCV000063155 likely benign not specified 2012-06-28 criteria provided, single submitter clinical testing 1093-6C>T in intron 10 of MAP2K2: This variant is not expected to have clinical significance because it has been identified in 0.23% (10/4324) of African Americ an chromosomes from a broad population by the NHLBI Exome Sequencing Project (ht tp://evs.gs.washington.edu/EVS/). In addition, splicing variants have not been r eported in Noonan syndrome.
GeneDx RCV000039471 SCV000513532 likely benign not specified 2017-06-29 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.
Invitae RCV000463260 SCV000561658 likely benign Rasopathy 2020-10-02 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000590120 SCV000699627 benign not provided 2016-08-15 criteria provided, single submitter clinical testing Variant summary: The MAP2K2 c.1093-6T>C variant involves the alteration of a conserved intronic nucleotide. Mutation Taster predicts a benign outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 9/21250 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.0031757 (9/2834). This frequency is about 1270 times the estimated maximal expected allele frequency of a pathogenic MAP2K2 variant (0.0000025), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. One clinical diagnostic laboratory has classified this variant as likely benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications. Taken together, this variant is classified as Benign.

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