ClinVar Miner

Submissions for variant NM_006939.4(SOS2):c.2057+19T>A

gnomAD frequency: 0.00015  dbSNP: rs544924513
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000616553 SCV000714097 likely benign not specified 2017-04-04 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 RCV000616553 SCV001361613 benign not specified 2019-08-26 criteria provided, single submitter clinical testing Variant summary: SOS2 c.2057+19T>A alters a nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 5/5 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 0.00032 in 155274 control chromosomes (gnomAD). The observed variant frequency is approximately 128 fold of the estimated maximal expected allele frequency for a pathogenic variant in SOS2 causing Noonan Syndrome and Related Conditions phenotype (2.5e-06), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.2057+19T>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 and classified the variant as likely benign. Based on the evidence outlined above, the variant was classified as benign.
Invitae RCV002062174 SCV002390746 likely benign Noonan syndrome 9 2024-01-31 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV002062174 SCV002763056 benign Noonan syndrome 9 criteria provided, single submitter clinical testing

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