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NM_000179.3(MSH6):c.354A>G (p.Thr118=) AND Carcinoma of colon

Germline classification:
Likely benign (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:
RCV001355723.2

Allele description [Variation Report for NM_000179.3(MSH6):c.354A>G (p.Thr118=)]

NM_000179.3(MSH6):c.354A>G (p.Thr118=)

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.354A>G (p.Thr118=)
HGVS:
  • NC_000002.12:g.47791020A>G
  • NG_007111.1:g.12874A>G
  • NM_000179.3:c.354A>GMANE SELECT
  • NM_001281492.2:c.237+7550A>G
  • NM_001281493.2:c.-383A>G
  • NM_001281494.2:c.-549A>G
  • NP_000170.1:p.Thr118=
  • NP_000170.1:p.Thr118=
  • LRG_219t1:c.354A>G
  • LRG_219:g.12874A>G
  • LRG_219p1:p.Thr118=
  • NC_000002.11:g.48018159A>G
  • NM_000179.2:c.354A>G
  • p.Thr118Thr
Links:
dbSNP: rs558590898
NCBI 1000 Genomes Browser:
rs558590898
Molecular consequence:
  • NM_001281493.2:c.-383A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001281494.2:c.-549A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001281492.2:c.237+7550A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000179.3:c.354A>G - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Carcinoma of colon (CRC)
Synonyms:
Colonic carcinoma; Colon carcinoma
Identifiers:
MONDO: MONDO:0002032; MedGen: C0699790

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001550681Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Likely 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), SCV001550681.1

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

Description

The MSH6 p.Thr118= variant was not identified in the literature nor was it identified in the COGR, Cosmic, MutDB, UMD-LSDB, Insight Colon Cancer Gene Variant Database, Zhejiang Colon Cancer Database, Mismatch Repair Genes Variant Database, or Insight Hereditary Tumors databases. The variant was identified in dbSNP (ID: rs558590898) as “With Likely benign allele”, ClinVar (as likely benign by Invitae, Partners HealthCare Personalized Medicine, Ambry Genetics, and Color), and Clinvitae (3x). The variant was identified in control databases in 4 of 246272 chromosomes at a frequency of 0.00002 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 1 of 15304 chromosomes (freq: 0.00007), European (Non-Finnish) in 2 of 111720 chromosomes (freq: 0.00002), and East Asian in 1 of 17248 chromosomes (freq: 0.000058); it was not observed in the Other, Latino, Ashkenazi Jewish, Finnish, and South Asian populations. The p.Thr118= variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. In addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) 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: Sep 29, 2024