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NM_001048174.2(MUTYH):c.264+11G>A 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:
RCV001354112.2

Allele description [Variation Report for NM_001048174.2(MUTYH):c.264+11G>A]

NM_001048174.2(MUTYH):c.264+11G>A

Gene:
MUTYH:mutY DNA glycosylase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p34.1
Genomic location:
Preferred name:
NM_001048174.2(MUTYH):c.264+11G>A
HGVS:
  • NC_000001.11:g.45333402C>T
  • NG_008189.1:g.12069G>A
  • NM_001048171.2:c.264+11G>A
  • NM_001048172.2:c.267+11G>A
  • NM_001048173.2:c.264+11G>A
  • NM_001048174.2:c.264+11G>AMANE SELECT
  • NM_001128425.2:c.348+11G>A
  • NM_001293190.2:c.309+11G>A
  • NM_001293191.2:c.297+11G>A
  • NM_001293192.2:c.-13+11G>A
  • NM_001293195.2:c.264+11G>A
  • NM_001293196.2:c.-13+11G>A
  • NM_001350650.2:c.-8+11G>A
  • NM_001350651.2:c.-8+11G>A
  • NM_012222.3:c.339+11G>A
  • LRG_220t1:c.348+11G>A
  • LRG_220:g.12069G>A
  • NC_000001.10:g.45799074C>T
  • NM_001048171.1:c.306+11G>A
  • NM_001128425.1:c.348+11G>A
Links:
dbSNP: rs139977567
NCBI 1000 Genomes Browser:
rs139977567
Molecular consequence:
  • NM_001048171.2:c.264+11G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001048172.2:c.267+11G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001048173.2:c.264+11G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001048174.2:c.264+11G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001128425.2:c.348+11G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001293190.2:c.309+11G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001293191.2:c.297+11G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001293192.2:c.-13+11G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001293195.2:c.264+11G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001293196.2:c.-13+11G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001350650.2:c.-8+11G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001350651.2:c.-8+11G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_012222.3:c.339+11G>A - intron variant - [Sequence Ontology: SO:0001627]
Observations:
2

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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001548645Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Likely benignunknownclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes2not 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), SCV001548645.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testingnot provided

Description

The MUTYH c.348+11G>A variant was identified in 1 of 110 proband chromosomes (frequency: 0.001) from individuals or families with lung cancer (Shinmura 2001). The variant was also identified in dbSNP (ID: rs139977567) as With Uncertain significance allele, ClinVar (classified as benign by GeneDx; classified as uncertain significance by Illumina), Clinvitae, Insight Colon Cancer Gene Variant Database, databases. The variant was not identified in UMD-LSDB database. The variant was identified in control databases in 445 (8 homozygous) of 277170 chromosomes at a frequency of 0.0016 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Consortium Feb 27, 2017). The variant occurs outside of the splicing consensus sequence and 1 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. 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 provided2not providednot providednot provided

Last Updated: Sep 29, 2024