Table 1 Descriptions of the variants in the APC, MLH1, MSH2 and PMS2 genes according to high impact and moderate impact on the Amazonian indigenous population (INDG) and continental populations (African (AFR), American (AMR), East Asian (EAS), European (EUR) and South Asian (SAS)) described in the 1000 Genomes database and GnomAD database.
Gene | ID SNP | Position | Var type | Region detailed | Impact predicted by SnpEff | INDG | AFR | EAS | AMR | EUR | SAS |
|---|---|---|---|---|---|---|---|---|---|---|---|
APC | rs2229992 | 112,827,157 | SNV | PROTEIN_STRUCTURAL_INTERACTION_LOCUS | High | 0,87 | 0,162 | 0,665 | 0,667 | 0,580 | 0,638 |
MSH2 | rs1060502002 | 47,410,332 | SNV | PROTEIN_STRUCTURAL_INTERACTION_LOCUS | High | 0,008 | 0,000 | 0,000 | 0,000 | – | 0,000 |
APC | rs41115 | 112,840,073 | SNV | SYNONYMOUS_CODING | High | 0,890 | 0,517 | 0,816 | 0,716 | 0,599 | 0,742 |
APC | rs864622761 | 112,842,683 | SNV | SYNONYMOUS_CODING | Moderate | 0,000 | 0,000 | 0,000 | 0,000 | – | 0,000 |
PMS2 | rs2228006 | 5,987,144 | SNV | NON_SYNONYMOUS_CODING | Moderate | 0,537 | 0,058 | 0,122 | 0,226 | 0,123 | 0,106 |
PMS2 | rs1805321 | 5,987,357 | SNV | NON_SYNONYMOUS_CODING | Moderate | 0,362 | 0,272 | 0,360 | 0,428 | 0,437 | 0,342 |
MSH2 | rs17217716 | 47,403,214 | SNV | NON_SYNONYMOUS_CODING | Moderate | 0,077 | 0,001 | 0,012 | 0,013 | 0,003 | 0,001 |
APC | rs459552 | 112,841,059 | SNV | NON_SYNONYMOUS_CODING | Moderate | 0,894 | 0,009 | 0,099 | 0,182 | 0,235 | 0,204 |
PMS2 | rs1805319 | 5,997,349 | SNV | SYNONYMOUS_CODING | Moderate | 0,580 | 0,144 | 0,121 | 0,252 | 0,164 | 0,196 |
MLH1 | rs55907433 | 5,997,349 | SNV | NON_SYNONYMOUS_CODING | Moderate | 0,000 | 0,009 | 0,000 | 0,001 | 0,000 | 0,000 |
MLH1 | rs1799977 | 37,012,077 | SNV | NON_SYNONYMOUS_CODING | Moderate | 0,086 | 0,039 | 0,026 | 0,169 | 0,325 | 0,131 |
PMS2 | rs1805324 | 5,986,899 | SNV | NON_SYNONYMOUS_CODING | Moderate | 0,000 | 0,001 | 0,000 | 0,009 | 0,032 | 0,002 |
MLH1 | rs2020873 | 37,050,534 | SNV | NON_SYNONYMOUS_CODING | Moderate | 0,008 | 0,107 | 0,000 | 0,006 | 0,000 | 0,000 |
APC | rs550945533 | 112,767,248 | SNV | NON_SYNONYMOUS_CODING | Moderate | 0,000 | 0,000 | 0,001 | 0,000 | 0,000 | 0,000 |
