ClinVar Miner

Submissions for variant NM_006939.4(SOS2):c.2786-6del

dbSNP: rs201957103
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Total submissions: 4
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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 RCV001175492 SCV001339085 benign not specified 2020-03-23 criteria provided, single submitter clinical testing Variant summary: SOS2 c.2786-6delT 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 0.23 in 31004 control chromosomes in the gnomAD database, including 9 homozygotes. The observed variant frequency is approximately 92155 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.2786-6delT in individuals affected with Noonan Syndrome and Related Conditions and no experimental evidence demonstrating its impact on protein function have been reported. No 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.
Invitae RCV001515860 SCV001724027 benign Noonan syndrome 9 2024-02-01 criteria provided, single submitter clinical testing
GeneDx RCV001712867 SCV001944916 benign not provided 2019-08-10 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001515860 SCV002763026 benign Noonan syndrome 9 criteria provided, single submitter clinical testing

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