ClinVar Miner

Submissions for variant NM_006939.4(SOS2):c.3769A>G (p.Asn1257Asp)

gnomAD frequency: 0.00020  dbSNP: rs150393358
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000652815 SCV000774687 likely benign Noonan syndrome 9 2024-01-24 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001805782 SCV002051284 likely benign not specified 2023-08-08 criteria provided, single submitter clinical testing Variant summary: SOS2 c.3769A>G (p.Asn1257Asp) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00016 in 251484 control chromosomes (gnomAD). The observed variant frequency is approximately 63 fold of 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.3769A>G in individuals affected with Noonan Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. One submitter has cited clinical-significance assessments for this variant to ClinVar after 2014 and has classified the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as likely benign.
Genome-Nilou Lab RCV000652815 SCV002762976 likely benign Noonan syndrome 9 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV003392500 SCV004134074 likely benign not provided 2022-12-01 criteria provided, single submitter clinical testing SOS2: BP4
PreventionGenetics, part of Exact Sciences RCV003918081 SCV004735446 likely benign SOS2-related condition 2022-10-27 criteria provided, single submitter clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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