ClinVar Miner

Submissions for variant NM_005633.3(SOS1):c.3391+7A>G (rs201982464)

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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000157004 SCV000206729 likely benign Noonan syndrome 2012-10-16 no assertion criteria provided clinical testing
ClinGen RASopathy Variant Curation Expert Panel RCV000228908 SCV000616506 benign Rasopathy 2017-04-18 reviewed by expert panel curation The filtering allele frequency of the c.3391+7A>G variant in the SOS1 gene is 0.193% (41/16108) of South Asian chromosomes by the Exome Aggregation Consortium, which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen RASopathy Expert Panel (BA1; PMID:29493581)
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000590714 SCV000227827 uncertain significance not provided 2015-01-19 criteria provided, single submitter clinical testing
GeneDx RCV000038550 SCV000171780 benign not specified 2013-03-14 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.
Illumina Clinical Services Laboratory,Illumina RCV000157004 SCV000430419 uncertain significance Noonan syndrome 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000300498 SCV000430420 uncertain significance Gingival fibromatosis 2016-06-14 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000590714 SCV000698634 benign not provided 2017-07-24 criteria provided, single submitter clinical testing Variant summary: The SOS1 c.3391+7A>G variant involves the alteration of a conserved intronic nucleotide. One in silico tool predicts a damaging 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. This variant was found in 94/118614 control chromosomes (1 homozygote) at a frequency of 0.0007925, which is approximately 26 times the estimated maximal expected allele frequency of a pathogenic SOS1 variant (0.00003), suggesting this variant is likely a benign polymorphism. Ths variant has been reported in affected individual and reported as a "disease-unrelated variant" by authors (Lepri_2011). In addition, multiple clinical diagnostic laboratories/reputable databases recently classified this variant as benign/VUS. Taken together, this variant is classified as benign.
Invitae RCV000228908 SCV000288966 benign Rasopathy 2017-03-22 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000038550 SCV000062228 benign not specified 2015-12-22 criteria provided, single submitter clinical testing c.3391+7A>G in intron 21 of SOS1: This variant is not expected to have clinical significance because it is not located within the splice consensus sequence. It has been identified in 0.3% (41/16108) of South Asian chromosomes including one homozygous individual and 0.07% (45/65182) European chromosomes by the Exome Ag gregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs201982464).
PreventionGenetics RCV000038550 SCV000311203 benign not specified criteria provided, single submitter clinical testing

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