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NM_000179.3(MSH6):c.3801+17T>C AND not provided

Germline classification:
Benign (1 submission)
Last evaluated:
Jan 4, 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:
RCV000590707.1

Allele description [Variation Report for NM_000179.3(MSH6):c.3801+17T>C]

NM_000179.3(MSH6):c.3801+17T>C

Gene:
MSH6:mutS homolog 6 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p16.3
Genomic location:
Preferred name:
NM_000179.3(MSH6):c.3801+17T>C
HGVS:
  • NC_000002.12:g.47806375T>C
  • NG_007111.1:g.28229T>C
  • NG_008397.1:g.104301A>G
  • NM_000179.3:c.3801+17T>CMANE SELECT
  • NM_001281492.2:c.3411+17T>C
  • NM_001281493.2:c.2895+17T>C
  • NM_001281494.2:c.2895+17T>C
  • LRG_219t1:c.3801+17T>C
  • LRG_219:g.28229T>C
  • NC_000002.11:g.48033514T>C
  • NM_000179.2:c.3801+17T>C
Links:
dbSNP: rs3136365
NCBI 1000 Genomes Browser:
rs3136365
Molecular consequence:
  • NM_000179.3:c.3801+17T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001281492.2:c.3411+17T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001281493.2:c.2895+17T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001281494.2:c.2895+17T>C - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000695889Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Benign
(Jan 4, 2016) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

LabCorp Variant Classification Summary - May 2015.docx

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Germ-line msh6 mutations in colorectal cancer families.

Kolodner RD, Tytell JD, Schmeits JL, Kane MF, Gupta RD, Weger J, Wahlberg S, Fox EA, Peel D, Ziogas A, Garber JE, Syngal S, Anton-Culver H, Li FP.

Cancer Res. 1999 Oct 15;59(20):5068-74.

PubMed [citation]
PMID:
10537275

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000695889.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Variant summary: This c.3801+17T>C variant affects a non-conserved intronic nucleotide at a location not widely known to affect normal splicing. 5/5 splice-site tools via Alamut predict that this variant does not affect normal splicing. In addition, ESEfinder also predicts that this variant does not affect ESE sites. This variant is found in 51/10276 African control chromosomes (including 1 homozygote) at a frequency of 0.00496, which is about 34 times greater than the maximal expected frequency of a pathogenic allele (0.0001421) in this gene, suggesting this variant is benign. In addition, two clinical laboratories have classified this variant as benign/likely benign. Taken together, this variant was classified as Benign.

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

Last Updated: Oct 8, 2024