ClinVar Miner

Submissions for variant NM_030662.3(MAP2K2):c.240G>A (p.Ala80=) (rs543217722)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen RASopathy Variant Curation Expert Panel RCV000523706 SCV000616586 likely benign Rasopathy 2017-05-09 reviewed by expert panel curation The filtering allele frequency of the c.240G>A (p.Ala80=) variant in the MAP2K2 gene is 0.0284% (9/16506) of South Asian chromosomes by the Exome Aggregation Consortium, which is a high enough frequency to be classified as likely benign based on thresholds defined by the ClinGen RASopathy Expert Panel (BS1; PMID:29493581)
GeneDx RCV000590354 SCV000515366 likely benign not provided 2017-09-11 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 RCV000590354 SCV000699633 benign not provided 2016-03-21 criteria provided, single submitter clinical testing Variant summary: The c.240G>A variant affects a non-conserved nucleotide, resulting in a synonymous change. Mutation taster predicts damaging outcome for this variant. 4/5 in silico programs via Alamut predict no significant change on RNA splicing sites. ESEfiner predicts changes of binding motifs for splicing enhancers. This variant is found in 10/120764 control chromosomes at a frequency of 0.0000828, predominalty observed in South Asian subpopulation in ExAC with MAF of 0.005453 (9/16506 chr), which significantly exceeds the maximal expected frequency of a pathogenic allele (0.0000025), suggesting this variant is benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical laboratories; nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant was classified as benign.
Invitae RCV000523706 SCV000776888 likely benign Rasopathy 2017-10-26 criteria provided, single submitter clinical testing

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