NM_000251.3(MSH2):c.198C>T (p.Tyr66=) AND Carcinoma of colon
- Germline classification:
- Likely benign (1 submission)
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Somatic classification
of clinical impact: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Somatic classification
of oncogenicity: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Record status:
- current
- Accession:
- RCV001354005.4
Allele description [Variation Report for NM_000251.3(MSH2):c.198C>T (p.Tyr66=)]
NM_000251.3(MSH2):c.198C>T (p.Tyr66=)
- Gene:
- MSH2:mutS homolog 2 [Gene - OMIM - HGNC]
- Variant type:
- single nucleotide variant
- Cytogenetic location:
- 2p21
- Genomic location:
- Preferred name:
- NM_000251.3(MSH2):c.198C>T (p.Tyr66=)
- Other names:
- p.Y66Y:TAC>TAT
- HGVS:
- NC_000002.12:g.47403389C>T
- NG_007110.2:g.5266C>T
- NG_095167.1:g.593C>T
- NM_000251.3:c.198C>TMANE SELECT
- NM_001258281.1:c.-1C>T
- NM_001406631.1:c.198C>T
- NM_001406632.1:c.198C>T
- NM_001406633.1:c.198C>T
- NM_001406634.1:c.198C>T
- NM_001406635.1:c.198C>T
- NM_001406636.1:c.198C>T
- NM_001406637.1:c.198C>T
- NM_001406638.1:c.198C>T
- NM_001406639.1:c.198C>T
- NM_001406640.1:c.198C>T
- NM_001406641.1:c.198C>T
- NM_001406642.1:c.198C>T
- NM_001406643.1:c.198C>T
- NM_001406644.1:c.198C>T
- NM_001406645.1:c.198C>T
- NM_001406646.1:c.198C>T
- NM_001406647.1:c.198C>T
- NM_001406648.1:c.198C>T
- NM_001406649.1:c.198C>T
- NM_001406650.1:c.198C>T
- NM_001406651.1:c.198C>T
- NM_001406652.1:c.198C>T
- NM_001406653.1:c.198C>T
- NM_001406654.1:c.-143C>T
- NM_001406655.1:c.198C>T
- NM_001406656.1:c.-798C>T
- NM_001406657.1:c.198C>T
- NM_001406658.1:c.-1121C>T
- NM_001406659.1:c.-1271C>T
- NM_001406660.1:c.-1468C>T
- NM_001406661.1:c.-1423C>T
- NM_001406662.1:c.-1340C>T
- NM_001406666.1:c.198C>T
- NM_001406669.1:c.-1271C>T
- NM_001406672.1:c.198C>T
- NM_001406674.1:c.198C>T
- NP_000242.1:p.Tyr66=
- NP_000242.1:p.Tyr66=
- NP_001393560.1:p.Tyr66=
- NP_001393561.1:p.Tyr66=
- NP_001393562.1:p.Tyr66=
- NP_001393563.1:p.Tyr66=
- NP_001393564.1:p.Tyr66=
- NP_001393565.1:p.Tyr66=
- NP_001393566.1:p.Tyr66=
- NP_001393567.1:p.Tyr66=
- NP_001393568.1:p.Tyr66=
- NP_001393569.1:p.Tyr66=
- NP_001393570.1:p.Tyr66=
- NP_001393571.1:p.Tyr66=
- NP_001393572.1:p.Tyr66=
- NP_001393573.1:p.Tyr66=
- NP_001393574.1:p.Tyr66=
- NP_001393575.1:p.Tyr66=
- NP_001393576.1:p.Tyr66=
- NP_001393577.1:p.Tyr66=
- NP_001393578.1:p.Tyr66=
- NP_001393579.1:p.Tyr66=
- NP_001393580.1:p.Tyr66=
- NP_001393581.1:p.Tyr66=
- NP_001393582.1:p.Tyr66=
- NP_001393584.1:p.Tyr66=
- NP_001393586.1:p.Tyr66=
- NP_001393595.1:p.Tyr66=
- NP_001393601.1:p.Tyr66=
- NP_001393603.1:p.Tyr66=
- LRG_218t1:c.198C>T
- LRG_218:g.5266C>T
- LRG_218p1:p.Tyr66=
- NC_000002.11:g.47630528C>T
- NM_000251.1:c.198C>T
- NM_000251.2:c.198C>T
- NM_001258281.1:c.-1C>T
- NR_176230.1:n.234C>T
- NR_176231.1:n.234C>T
- NR_176232.1:n.234C>T
- NR_176233.1:n.234C>T
- NR_176234.1:n.234C>T
- NR_176235.1:n.234C>T
- NR_176236.1:n.234C>T
- NR_176237.1:n.234C>T
- NR_176238.1:n.234C>T
- NR_176239.1:n.234C>T
- NR_176240.1:n.234C>T
- NR_176241.1:n.234C>T
- NR_176242.1:n.234C>T
- NR_176243.1:n.234C>T
- NR_176244.1:n.234C>T
- NR_176245.1:n.234C>T
- NR_176246.1:n.234C>T
- NR_176247.1:n.234C>T
- NR_176248.1:n.234C>T
- NR_176249.1:n.234C>T
- NR_176250.1:n.234C>T
- p.Y66Y
This HGVS expression did not pass validation- Links:
- dbSNP: rs730881784
- NCBI 1000 Genomes Browser:
- rs730881784
- Molecular consequence:
- NM_001258281.1:c.-1C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406654.1:c.-143C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406656.1:c.-798C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406658.1:c.-1121C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406659.1:c.-1271C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406660.1:c.-1468C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406661.1:c.-1423C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406662.1:c.-1340C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406669.1:c.-1271C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NR_176230.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_176231.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_176232.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_176233.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_176234.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_176235.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_176236.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_176237.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_176238.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_176239.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_176240.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_176241.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_176242.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_176243.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_176244.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_176245.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_176246.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_176247.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_176248.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_176249.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_176250.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NM_000251.3:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406631.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406632.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406633.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406634.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406635.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406636.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406637.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406638.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406639.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406640.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406641.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406642.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406643.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406644.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406645.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406646.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406647.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406648.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406649.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406650.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406651.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406652.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406653.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406655.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406657.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406666.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406672.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406674.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
Condition(s)
- Name:
- Carcinoma of colon (CRC)
- Synonyms:
- Colonic carcinoma; Colon carcinoma
- Identifiers:
- MONDO: MONDO:0002032; MedGen: C0699790
Assertion and evidence details
Submission Accession | Submitter | Review Status (Assertion method) | Clinical Significance (Last evaluated) | Origin | Method | Citations |
---|---|---|---|---|---|---|
SCV000592454 | Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)
| no assertion criteria provided | Likely benign | unknown | clinical testing |
Summary from all submissions
Ethnicity | Origin | Affected | Individuals | Families | Chromosomes tested | Number Tested | Family history | Method |
---|---|---|---|---|---|---|---|---|
not provided | unknown | yes | not provided | not provided | not provided | not provided | not provided | clinical testing |
Details of each submission
From Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV000592454.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | not provided |
Description
MSH2, EXON01, c.198C>T, p.= (p.Tyr66Tyr), Heterozygous, Likely benign rnrnThe MSH2 c.198C>T variant was not identified in the literature nor was it identified in the COSMIC, “Mismatch Repair Genes Variant Database”, “MMR Gene Unclassified Variants Database”, InSiGHT Colon Cancer Gene Variant Database (LOVD), Zhejiang Colon Cancer Database (LOVD) and GeneInsight - COGR database. The variant was identified in dbSNP (ID: rs730881784) as “With Likely benign allele”, ClinVar database (classified as benign by GeneDx and likely benign by Ambry Genetics and Invitae) and UMD (1x with an “unclassified variant” classification). This variant was identified in the Exome Aggregation Consortium database (August 8, 2016) in 11 of 83058 chromosomes (freq. 0.0001) in the following populations: European in 11 of 47956 chromosomes (freq. 0.0002), increasing the likelihood that this may be a low frequency benign variant in certain populations of origin. The p.Tyr66Tyr 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. The variant occurs outside of the splicing consensus sequence and 2 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.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
Last Updated: Oct 8, 2024