ClinVar Miner

Submissions for variant NM_006939.4(SOS2):c.1609G>T (p.Ala537Ser)

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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001251318 SCV001426868 benign not specified 2020-07-20 criteria provided, single submitter clinical testing Variant summary: SOS2 c.1609G>T (p.Ala537Ser) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 6.8e-05 in 251012 control chromosomes in the gnomAD database, including 1 homozygote. The observed variant frequency is approximately 27-fold the estimated maximal expected allele frequency for a pathogenic variant in SOS2 causing Noonan Syndrome phenotype (2.5e-06), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.1609G>T in individuals affected with Noonan Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. No other clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as benign.

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