ClinVar Miner

Submissions for variant NM_030662.4(MAP2K2):c.303+12G>A

gnomAD frequency: 0.00030  dbSNP: rs376432107
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV000039478 SCV000063163 likely benign not specified 2012-11-20 criteria provided, single submitter clinical testing 303+12G>A in intron 2 of MAP2K2: This variant is not expected to have clinical s ignificance because it is not located within the splice consensus sequence. It h as been identified in 0.09% (4/4406) of African American chromosomes from a broa d population by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu /EVS).
GeneDx RCV000039478 SCV000728671 benign not specified 2017-04-03 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000039478 SCV001338522 benign not specified 2020-04-13 criteria provided, single submitter clinical testing Variant summary: MAP2K2 c.303+12G>A alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 4/4 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 6e-05 in 249174 control chromosomes in the gnomAD database, including 1 homozygote. The observed variant frequency is approximately 24 fold of the estimated maximal expected allele frequency for a pathogenic variant in MAP2K2 causing Noonan Syndrome And Related Conditions phenotype (2.5e-06), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.303+12G>A in individuals affected with Noonan Syndrome And Related Conditions and no experimental evidence demonstrating its impact on protein function have been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. One laboratory classified the variant as benign. Based on the evidence outlined above, the variant was classified as benign.
Labcorp Genetics (formerly Invitae), Labcorp RCV002054765 SCV002491514 likely benign RASopathy 2023-12-19 criteria provided, single submitter clinical testing

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