ClinVar Miner

Submissions for variant NM_006939.4(SOS2):c.3489+19C>T

gnomAD frequency: 0.00700  dbSNP: rs149825446
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Total submissions: 6
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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 RCV000586388 SCV000698743 benign not provided 2017-04-11 criteria provided, single submitter clinical testing Variant summary: The SOS2 c.3489+19C>T 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 SRp40 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 0.0025052 (281/112168 control chromosomes [4 homozygotes]), which is approximately 1002 times the estimated maximal expected allele frequency of a pathogenic SOS2 variant (0.0000025), suggesting this variant is likely a benign polymorphism. The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical diagnostic laboratories, nor has it been evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as benign.
GeneDx RCV000600372 SCV000714417 benign not specified 2017-04-10 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV002061987 SCV002415533 benign Noonan syndrome 9 2024-01-31 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV002061987 SCV002506026 benign Noonan syndrome 9 2023-10-05 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV002061987 SCV002762997 benign Noonan syndrome 9 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002061987 SCV002805625 likely benign Noonan syndrome 9 2021-09-30 criteria provided, single submitter clinical testing

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