NM_005732.4(RAD50):c.2670G>A (p.Gln890=) AND not specified

Clinical significance:Benign/Likely benign (Last evaluated: Mar 30, 2018)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000212913.2

Allele description [Variation Report for NM_005732.4(RAD50):c.2670G>A (p.Gln890=)]

NM_005732.4(RAD50):c.2670G>A (p.Gln890=)

Gene:
RAD50:RAD50 double strand break repair protein [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q31.1
Genomic location:
Preferred name:
NM_005732.4(RAD50):c.2670G>A (p.Gln890=)
Other names:
p.Q890Q:CAG>CAA
HGVS:
  • NC_000005.10:g.132604951G>A
  • NG_021151.1:g.53028G>A
  • NG_021151.2:g.52975G>A
  • NM_005732.4:c.2670G>AMANE SELECT
  • NP_005723.2:p.Gln890=
  • LRG_312t1:c.2670G>A
  • LRG_312:g.52975G>A
  • LRG_312p1:p.Gln890=
  • NC_000005.9:g.131940643G>A
  • NM_005732.3:c.2670G>A
  • p.Q890Q
Links:
dbSNP: rs112241748
NCBI 1000 Genomes Browser:
rs112241748
Molecular consequence:
  • NM_005732.4:c.2670G>A - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
1

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000211606GeneDxcriteria provided, single submitter
Benign
(Jan 23, 2014)
germlineclinical testing

Citation Link,

SCV000860259EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Likely benign
(Mar 30, 2018)
germlineclinical testing

Citation Link,

SCV000918120Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Benign
(Jan 8, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown1not providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000211606.10

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

Description

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.

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

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000860259.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000918120.1

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

Description

Variant summary: The RAD50 c.2670G>A (p.Gln890Gln) variant involves the alteration of a non-conserved nucleotide causing a synonymous change and 4/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may alter ESE binding. However, these predictions have yet to be confirmed by functional studies. This variant was found in 176/277102 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.006285 (151/24026). This frequency is about 101 times the estimated maximal expected allele frequency of a pathogenic RAD50 variant (0.0000625), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. In addition, multiple clinical diagnostic laboratories classified this variant as benign/likely benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications; nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as benign.

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

Last Updated: Nov 27, 2021

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