ClinVar Miner

Submissions for variant NM_006939.4(SOS2):c.88-6T>C

gnomAD frequency: 0.31349  dbSNP: rs12888783
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000586765 SCV000524329 benign not provided 2016-09-29 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 RCV000586765 SCV000698752 benign not provided 2017-04-17 criteria provided, single submitter clinical testing Variant summary: The SOS2 c.88-6T>C variant involves the alteration of a non-conserved intronic nucleotide. One in silico tool predicts a benign outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant of interest has been found in a large, broad control population, ExAC in 41472/120656 control chromosomes (7805 homozygotes) at a frequency of 0.343721, which is approximately 137488 times the estimated maximal expected allele frequency of a pathogenic SOS2 variant (0.0000025), suggesting this variant is likely a benign polymorphism. In addition, one clinical diagnostic laboratory classified this variant as benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications; nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as benign.
Invitae RCV001515862 SCV001724029 benign Noonan syndrome 9 2024-02-01 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001515862 SCV002763154 benign Noonan syndrome 9 criteria provided, single submitter clinical testing
Clinical Genetics, Academic Medical Center RCV001706628 SCV001919605 benign not specified no assertion criteria provided clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ RCV001706628 SCV001952931 benign not specified no assertion criteria provided clinical testing

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