rs2020912
A SNP in the MSH6 gene on chromosome 2. Its most notable genotype is C;T: unclear if associated with hereditary nonpolyposis colorectal cancer (HNPCC5)
- Gene
- MSH6
- Location
- Chr 247,800,616 (GRCh38)
- Highest magnitude
- 2.5Worth knowing
- Tested on
- 23andMe, AncestryDNA, FamilyTreeDNA
- Minor allele frequency
- <1%
Genotypes
As shown in 23andMe and AncestryDNA files.
- C;TMost notableBadunclear if associated with hereditary nonpolyposis colorectal cancer (HNPCC5)
- T;TGoodcommon in clinvar
On SNPedia: (C;T), (T;T). Magnitude rates how notable a genotype is from 0 to 10, not how risky it is.
Frequency
Share of each genotype in 10 HapMap populations.
- AverageC;T 2% T;T 98%
- European ancestry (Utah)C;T 2% T;T 98%
- Han Chinese (Beijing)C;T 2% T;T 99%
- Japanese (Tokyo)C;T <1% T;T 99%
- Yoruba (Nigeria)C;T 2% T;T 98%
- African ancestry (Southwest US)C;T 4% T;T 96%
- Chinese (Denver)C;T <1% T;T 99%
- Gujarati IndianC;T 2% T;T 98%
- Luhya (Kenya)C;T <1% T;T 99%
- Maasai (Kenya)C;T <1% T;T 99%
- TuscanC;T 6% T;T 94%
Related
Other MSH6 SNPs
- rs587776706T;TMismatch repair cancer syndrome (predicted)Very important
- rs1800937A;CLynch syndrome, pathogenic mutationVery important
- rs63749821-;TALikely miscall in Ancestry data; otherwise, Lynch syndrome, pathogenic mutationVery important
- rs63749843C;TLynch syndrome, pathogenic mutationVery important
- rs63749873C;GLynch syndrome, pathogenic mutationVery important
- rs63749874-;AAGALynch syndrome, pathogenic mutationVery important
- rs63749919A;GLynch syndromeVery important
- rs63749938-;ALynch Syndrome, pathogenic mutationVery important
Notes
From SNPedia
Show notes, about 120 words
rs2020912 is a SNP in the MSH6 gene on chromosome 2, which (as a gene) has been associated with hereditary nonpolyposis colorectal cancer (HNPCC). It is not clear whether this variant predisposes individuals to cancers such as colorectal cancer. In ClinVar, some entries list it as pathogenic, most list it as benign, and one lists it as likely to be benign. Even so, this variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. See also OMIM 600678.0006
C;T
This variant is probably benign, but there is a possibility it is associated with hereditary nonpolyposis colorectal cancer type-5 (HNPCC5).
Source and license
Adapted from rs2020912 on SNPedia, using a snapshot taken October 16, 2026. SNPedia content is shared under CC BY-NC-SA 3.0 US, and this page is shared under the same license.
SNPedia is a community-edited wiki. Its entries can be incomplete, out of date or wrong, and nothing here is a diagnosis or medical advice. Magnitude is a community rating of how interesting a genotype is, not a risk score.