NM_005236.3(ERCC4):c.2647G>A (p.Glu883Lys) AND not provided

Clinical significance:Likely benign

Review status:(0/4) 0 stars out of maximum of 4 stars

no assertion criteria provided

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001358163.1

Allele description [Variation Report for NM_005236.3(ERCC4):c.2647G>A (p.Glu883Lys)]

NM_005236.3(ERCC4):c.2647G>A (p.Glu883Lys)

Gene:
ERCC4:ERCC excision repair 4, endonuclease catalytic subunit [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p13.12
Genomic location:
Preferred name:
NM_005236.3(ERCC4):c.2647G>A (p.Glu883Lys)
HGVS:
  • NC_000016.10:g.13948243G>A
  • NG_011442.1:g.33087G>A
  • NM_005236.3:c.2647G>AMANE SELECT
  • NP_005227.1:p.Glu883Lys
  • LRG_463t1:c.2647G>A
  • LRG_463:g.33087G>A
  • NC_000016.9:g.14042100G>A
  • NM_005236.2:c.2647G>A
Protein change:
E883K
Links:
dbSNP: rs201652412
NCBI 1000 Genomes Browser:
rs201652412
Molecular consequence:
  • NM_005236.3:c.2647G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001553829Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria providedLikely benignunknownclinical testing

Summary from all submissions

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

Details of each submission

From Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001553829.1

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

Description

The ERCC4 p.Glu883Lys variant was not identified in the literature nor was it identified in ClinVar or LOVD 3.0. The variant was identified in dbSNP (ID: rs201652412) and in control databases in 134 of 268246 chromosomes (2 homozygous) at a frequency of 0.0004995 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: South Asian in 90 of 30526 chromosomes (freq: 0.002948), Other in 5 of 6702 chromosomes (freq: 0.000746), Ashkenazi Jewish in 6 of 9858 chromosomes (freq: 0.000609), European (non-Finnish) in 31 of 118102 chromosomes (freq: 0.000263) and Latino in 2 of 35108 chromosomes (freq: 0.000057), but was not observed in the African, East Asian, or European (Finnish) populations. The p.Glu883 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; however, this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.

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

Last Updated: May 16, 2021

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