NM_005633.4(SOS1):c.1719T>C (p.Asp573=) AND not provided

Germline classification:
Likely benign (1 submission)
Last evaluated:
Aug 1, 2016
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000589104.1

Allele description [Variation Report for NM_005633.4(SOS1):c.1719T>C (p.Asp573=)]

NM_005633.4(SOS1):c.1719T>C (p.Asp573=)

Gene:
SOS1:SOS Ras/Rac guanine nucleotide exchange factor 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p22.1
Genomic location:
Preferred name:
NM_005633.4(SOS1):c.1719T>C (p.Asp573=)
HGVS:
  • NC_000002.12:g.39022709A>G
  • NG_007530.1:g.102755T>C
  • NM_001382394.1:c.1698T>C
  • NM_001382395.1:c.1719T>C
  • NM_005633.4:c.1719T>CMANE SELECT
  • NP_001369323.1:p.Asp566=
  • NP_001369324.1:p.Asp573=
  • NP_005624.2:p.Asp573=
  • NP_005624.2:p.Asp573=
  • LRG_754t1:c.1719T>C
  • LRG_754:g.102755T>C
  • LRG_754p1:p.Asp573=
  • NC_000002.11:g.39249850A>G
  • NM_005633.3:c.1719T>C
Links:
dbSNP: rs746674452
NCBI 1000 Genomes Browser:
rs746674452
Molecular consequence:
  • NM_001382394.1:c.1698T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001382395.1:c.1719T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_005633.4:c.1719T>C - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:
none provided; RECLASSIFIED - ADRA2C POLYMORPHISM; RECLASSIFIED - ADRB1 POLYMORPHISM
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000698616Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Likely benign
(Aug 1, 2016) 		germlineclinical testing

LabCorp Variant Classification Summary - May 2015.docx

Citation Link

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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, SCV000698616.1

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

Description

Variant summary: The SOS1 c.1719T>C (p.Asp573Asp) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant. 3/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect ESE sites. However, these predictions have yet to be confirmed by functional studies. This variant was found in 3/121360 control chromosomes, predominantly observed in the East Asian subpopulation at a frequency of 0.0003467 (3/8652). This frequency is about 12 times the estimated maximal expected allele frequency of a pathogenic SOS1 variant (0.00003), suggesting this is likely a benign polymorphism found primarily in the populations of East Asian origin. The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical diagnostic laboratories; nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as Likely benign until more evidence becomes available.

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

Last Updated: Mar 11, 2025