ClinVar Miner

Submissions for variant NM_005633.4(SOS1):c.213+16T>C

gnomAD frequency: 0.00128  dbSNP: rs150536159
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000128193 SCV000171785 benign not specified 2014-05-09 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.
PreventionGenetics, part of Exact Sciences RCV000128193 SCV000311190 likely benign not specified criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000128193 SCV001448452 benign not specified 2020-11-16 criteria provided, single submitter clinical testing Variant summary: SOS1 c.213+16T>C 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 0.00025 in 251338 control chromosomes, predominantly at a frequency of 0.0036 within the African or African-American subpopulation in the gnomAD database. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 120 fold of the estimated maximal expected allele frequency for a pathogenic variant in SOS1 causing Noonan Syndrome phenotype (3e-05), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African or African-American origin. To our knowledge, no occurrence of c.213+16T>C in individuals affected with Noonan Syndrome 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV002055813 SCV002427403 benign RASopathy 2024-01-29 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV002467581 SCV002763603 benign Noonan syndrome 4 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV002467580 SCV002763604 benign Fibromatosis, gingival, 1 criteria provided, single submitter clinical testing

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