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NM_000179.3(MSH6):c.3556+36_3556+39del AND not provided

Germline classification:
Benign (1 submission)
Last evaluated:
Apr 20, 2017
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:
RCV000588085.2

Allele description [Variation Report for NM_000179.3(MSH6):c.3556+36_3556+39del]

NM_000179.3(MSH6):c.3556+36_3556+39del

Gene:
MSH6:mutS homolog 6 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
2p16.3
Genomic location:
Preferred name:
NM_000179.3(MSH6):c.3556+36_3556+39del
HGVS:
  • NC_000002.12:g.47805063_47805066del
  • NG_007111.1:g.26917_26920del
  • NG_008397.1:g.105613_105616del
  • NM_000179.3:c.3556+36_3556+39delMANE SELECT
  • NM_001281492.2:c.3166+36_3166+39del
  • NM_001281493.2:c.2650+36_2650+39del
  • NM_001281494.2:c.2650+36_2650+39del
  • LRG_219:g.26917_26920del
  • NC_000002.11:g.48032202_48032205del
  • NM_000179.2:c.3556+36_3556+39delGTCA
  • NM_000179.3:c.3556+36_3556+39delGTCAMANE SELECT
Links:
dbSNP: rs55684722
NCBI 1000 Genomes Browser:
rs55684722
Molecular consequence:
  • NM_000179.3:c.3556+36_3556+39del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001281492.2:c.3166+36_3166+39del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001281493.2:c.2650+36_2650+39del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001281494.2:c.2650+36_2650+39del - intron variant - [Sequence Ontology: SO:0001627]

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
SCV000695873Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Benign
(Apr 20, 2017) 		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, SCV000695873.1

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

Description

Variant summary: The MSH6 c.3556+36_3556+39delGTCA variant involves the deletion of 4 intronic nucleotides. One in silico tool predicts a benign outcome for this variant. 2/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 18/120584 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.001646 (17/10328). This frequency is about 12 times the estimated maximal expected allele frequency of a pathogenic MSH6 variant (0.0001421), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. In addition, one clinical diagnostic laboratory/reputable database has classified this variant as 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: Oct 8, 2024