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NM_013975.4(LIG3):c.2961G>A (p.Ala987=) AND not provided

Germline classification:
Benign (1 submission)
Last evaluated:
Aug 29, 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:
RCV000586190.1

Allele description [Variation Report for NM_013975.4(LIG3):c.2961G>A (p.Ala987=)]

NM_013975.4(LIG3):c.2961G>A (p.Ala987=)

Gene:
LIG3:DNA ligase 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q12
Genomic location:
Preferred name:
NM_013975.4(LIG3):c.2961G>A (p.Ala987=)
HGVS:
  • NC_000017.11:g.35004437G>A
  • NG_029221.1:g.28940G>A
  • NM_013975.4:c.2961G>AMANE SELECT
  • NP_039269.2:p.Ala987=
  • NC_000017.10:g.33331456G>A
  • NM_013975.3:c.2961G>A
Links:
dbSNP: rs76122405
NCBI 1000 Genomes Browser:
rs76122405
Molecular consequence:
  • NM_013975.4:c.2961G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:
none provided
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
SCV000699350Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Benign
(Aug 29, 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, SCV000699350.1

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

Description

Variant summary: The LIG3 c.2961G>A (p.Ala987Ala) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. Mutation taster predicts a damaging outcome for this substitution while 4/5 splice site tool predict the variant not to have an impact on normal splicing. This variant was found in 488/121302 control chromosomes (9 homozygotes), predominantly observed in the East Asian subpopulation at a frequency of 0.0215029 (186/8650). This frequency greatly exceeds the estimated maximal expected allele frequency of a pathogenic LIG3 variant (0.00001), suggesting this is likely a benign polymorphism found primarily in 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. Considering the synonymous nature and the high prevalence of the variant in the East Asian subpopulation, it was classified as benign.

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

Last Updated: Dec 24, 2023