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NM_000179.3(MSH6):c.*11T>C AND Lynch syndrome

Germline classification:
Uncertain significance (1 submission)
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001355760.1

Allele description [Variation Report for NM_000179.3(MSH6):c.*11T>C]

NM_000179.3(MSH6):c.*11T>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.*11T>C
HGVS:
  • NC_000002.12:g.47806871T>C
  • NG_007111.1:g.28725T>C
  • NG_008397.1:g.103805A>G
  • NM_000179.3:c.*11T>CMANE SELECT
  • NM_001281492.2:c.*11T>C
  • NM_001281493.2:c.*11T>C
  • NM_001281494.2:c.*11T>C
  • LRG_219t1:c.*11T>C
  • LRG_219:g.28725T>C
  • NC_000002.11:g.48034010T>C
  • NM_000179.2:c.*11T>C
Links:
dbSNP: rs757708396
NCBI 1000 Genomes Browser:
rs757708396
Molecular consequence:
  • NM_000179.3:c.*11T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001281492.2:c.*11T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001281493.2:c.*11T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001281494.2:c.*11T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
Observations:
1

Condition(s)

Name:
Lynch syndrome
Identifiers:
MONDO: MONDO:0005835; MedGen: C4552100

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001550729Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Uncertain significanceunknownclinical testing

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes1not 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), SCV001550729.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The MSH6 c.*11T>C variant was not identified in the literature nor was it identified in the ClinVar or UMD-LSDB databases. The variant was identified in dbSNP (ID: rs757708396). The variant was identified in control databases in 2 of 245696 chromosomes at a frequency of 0.000008 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: Latino in 1 of 33520 chromosomes (freq: 0.00003) and European in 1 of 111462 chromosomes (freq: 0.000009), but not in the African, Other, Ashkenazi Jewish, East Asian, Finnish, or South Asian populations. 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. This variant is classified as a variant of uncertain significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Sep 16, 2024