NM_006939.4(SOS2):c.3755_3757del (p.Ile1252del) AND not specified

Clinical significance:Benign (Last evaluated: Jul 27, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_006939.4(SOS2):c.3755_3757del (p.Ile1252del)]

NM_006939.4(SOS2):c.3755_3757del (p.Ile1252del)

SOS2:SOS Ras/Rho guanine nucleotide exchange factor 2 [Gene - OMIM - HGNC]
Variant type:
Cytogenetic location:
Genomic location:
Preferred name:
NM_006939.4(SOS2):c.3755_3757del (p.Ile1252del)
  • NC_000014.9:g.50118587_50118589del
  • NG_051073.1:g.118106_118108del
  • NM_006939.4:c.3755_3757delMANE SELECT
  • NP_008870.2:p.Ile1252del
  • NC_000014.8:g.50585304_50585306del
  • NC_000014.8:g.50585305_50585307del
  • NM_006939.2:c.3755_3757del
  • NM_006939.2:c.3755_3757delTTA
  • NM_006939.3:c.3755_3757delTTA
Protein change:
dbSNP: rs775506222
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_006939.4:c.3755_3757del - inframe_deletion - [Sequence Ontology: SO:0001822]


MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV001426823Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
(Jul 27, 2020)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001426823.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided


Variant summary: SOS2 c.3755_3757delTTA (p.Ile1252del) results in an in-frame deletion that is predicted to remove 1 amino acid from the encoded protein. The variant allele was found at a frequency of 0.00013 in 251484 control chromosomes, predominantly at a frequency of 0.0014 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 560 fold of the estimated maximal expected allele frequency for a pathogenic variant in SOS2 causing Noonan Syndrome phenotype (2.5e-06), 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.3755_3757delTTA in individuals affected with Noonan Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. Two ClinVar submitters (evaluation after 2014) cite the variant as likely benign (n=1) and as uncertain significance n=1). Based on the evidence outlined above, the variant was classified as benign.

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 8, 2021

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