ClinVar Miner

Submissions for variant NM_006939.4(SOS2):c.3490-18A>C

gnomAD frequency: 0.14981  dbSNP: rs79858475
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000587777 SCV000525709 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 RCV000587777 SCV000698744 benign not provided 2017-04-11 criteria provided, single submitter clinical testing Variant summary: The SOS2 c.3490-18A>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. ESE Finder predicts the variant may create an SRp55 ESE site at the locus. However, these predictions have yet to be confirmed by functional studies. This variant was found in the large control database ExAC at a frequency of 0.1074677 (9973/92800 control chromosomes [681 homozygotes]), which is approximately 42987 times the estimated maximal expected allele frequency of a pathogenic SOS2 variant (0.0000025), strong evidence that 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 has it been evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as benign.
Labcorp Genetics (formerly Invitae), Labcorp RCV002058933 SCV002401504 benign Noonan syndrome 9 2025-02-04 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV002058933 SCV002762996 benign Noonan syndrome 9 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV000587777 SCV005288767 benign not provided criteria provided, single submitter not provided

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