ClinVar Miner

Submissions for variant NM_006939.4(SOS2):c.3813G>A (p.Pro1271=) (rs2227276)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000589171 SCV000525683 benign not provided 2016-09-28 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 RCV000589171 SCV000698745 benign not provided 2017-04-11 criteria provided, single submitter clinical testing Variant summary: The SOS2 c.3813G>A (p.Pro1271Pro) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may introduce an SF2/ASF 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 0.1980044 (24031/121366 control chromosomes [2718 homozygotes]), which is approximately 79202 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, multiple clinical diagnostic laboratories/reputable databases 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.
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV001195556 SCV001365947 benign not specified 2018-12-27 criteria provided, single submitter clinical testing p.Pro1271Pro in exon 23 of SOS2: This variant is not expected to have clinical significance because it does not alter an amino acid residue, is not located within the splice consensus sequence, and has been identified in 44.43% (3835/8632) of East Asian chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs2227276).
Invitae RCV001518639 SCV001727373 benign Noonan syndrome 9 2020-11-27 criteria provided, single submitter clinical testing

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