ClinVar Miner

Submissions for variant NM_006939.4(SOS2):c.2162-10C>T

gnomAD frequency: 0.00042  dbSNP: rs375702667
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000538946 SCV000656013 likely benign Noonan syndrome 9 2024-01-11 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001175095 SCV001338665 benign not specified 2020-04-27 criteria provided, single submitter clinical testing Variant summary: SOS2 c.2162-10C>T 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 0.00057 in 250014 control chromosomes (gnomAD). The observed variant frequency is approximately 229 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.2162-10C>T in individuals affected with Noonan Syndrome And Related Conditions and no experimental evidence demonstrating its impact on protein function have been reported. Co-occurrence with another pathogenic variant has been reported (PTPN11 c.844A>G, p.I282V) for this variant in our internal database. One ClinVar submitter (evaluation after 2014) cite the variant as likely benign. Based on the evidence outlined above, the variant was classified as benign.
GeneDx RCV001675932 SCV001894043 benign not provided 2018-07-27 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000538946 SCV002763053 benign Noonan syndrome 9 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003925721 SCV004738201 benign SOS2-related disorder 2019-09-26 no assertion criteria provided clinical testing This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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