Table 3.
Minor allele frequencies (MAFs) of clinically associated single nucleotide polymorphisms in African, US and Asian populations.
| MAF | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene | rsID | Minor allele | Polymorphism (NTpos; AA change) | Xhosa (n = 109) | CMA (n = 67) | Yoruba (n = 60) | Luhya (n = 89) | Maasai (n = 143) | Caucasian (n = 60) | Chinese (n = 45) | Hispanic (n = 23) | AAm (n = 24) | |
| ABC transporters | ABCB1 | rs2229109 | A | 1199G > A;S400N | 0.0 | 0.0 | 0.0 | NA | 0.0 | 0.03 | 0.0 | 0.0 | 0.0 |
| ABCB1 | rs9282564 | G | 61A > G; N21D | 0.0 | 0.0 | 0.0 | NA | NA | 0.1 | 0.0 | 0.07 | 0.0 | |
| ABCB1 | rs1045642 | C | 3435C > T | 0.89 | 0.8 | 0.88 | NA | 0.84 | 0.43 | 0.58 | 0.45 | 0.84 | |
| ABCB1 | rs4148740 | G | 12386379A > G | 0.14 | 0.17 | 0.13 | NA | NA | 0.1 | 0.02 | NA | 0.15 | |
| ABCB1 | rs7787082 | A | 12391327G > A | 0.69 | 0.61 | 0.68 | 0.71 | 0.62 | 0.18 | 0.46 | NA | 0.56 | |
| ABCB1 | rs2032583 | G | 12394837A > G | 0.14 | 0.18 | 0.25 | 0.25 | 0.23 | 0.16 | 0.03 | 0.04 | 0.15 | |
| ABCB1 | rs3789243 | G | 12455162A > G | 0.63 | 0.61 | 0.41 | 0.58 | 0.44 | 0.43 | 0.72 | NA | 0.6 | |
| ABCB1 | rs1128503 | T | 1236C > T | 0.13 | 0.23 | 0.12 | 0.11 | 0.14 | 0.39 | 0.68 | 0.54 | 0.06 | |
| ABCB1 | rs10248420 | G | 12399262A > G | 0.59 | 0.56 | 0.59 | 0.64 | 0.56 | 0.17 | 0.48 | 0.12 | 0.53 | |
| ABCB1 | rs2235041 | A | 12400010G > A | 0.12 | 0.07 | 0.12 | 0.1 | 0.1 | 0.0 | 0.0 | 0.0 | 0.14 | |
| ABCC2 | rs8187707 | T | 4488C > T;H1496H | 0.08 | 0.08 | 0.0 | 0.06 | 0.09 | 0.04 | 0.0 | 0.0 | 0.02 | |
| ABCC2 | rs2273697 | A | 1249G > A;V417I | 0.11 | 0.18 | 0.21 | 0.2 | 0.23 | 0.23 | 0.07 | 0.15 | 0.23 | |
| ABCC2 | rs717620 | T | -24C > T | 0.03 | 0.04 | 0.04 | 0.02 | 0.04 | 0.18 | 0.22 | 0.23 | 0.06 | |
| Phase I | CYP2B6 | rs3745274 | T | 516G > T;Q172H, *6 | 0.2 | 0.23 | 0.45 | 0.31 | 0.37 | 0.25 | 0.15 | 0.27 | 0.46 |
| CYP2B6 | rs28399499 | C | 983T > C;I328T, *18 | 0.17 | 0.09 | 0.04 | 0.07 | 0.02 | 0.0 | 0.0 | 0.0 | 0.03 | |
| CYP2B6 | rs36079186 | C | 593T > C; M198T, *27 | 0.0 | 0.0 | NA | NA | NA | NA | NA | NA | NA | |
| CYP2C18 | rs7896133 | A | 15213256G > A | 0.2 | 0.2 | 0.12 | 0.11 | 0.16 | 0.07 | 0.08 | NA | 0.1 | |
| CYP2C18 | rs2860840 | T | 15243758C > T | 0.0 | 0.09 | 0 | 0.01 | 0.06 | 0.35 | 0.23 | 0.28 | 0.09 | |
| CYP2C18 | rs10509675 | A | 15237414G > A | 0.15 | 0.09 | 0.27 | 0.18 | 0.17 | 0.21 | 0.02 | NA | 0.13 | |
| CYP2C19 | rs4917623 | C | 15358094T > C | 0.11 | 0.2 | 0.18 | 0.16 | 0.29 | 0.49 | 0.6 | NA | 0.1 | |
| CYP2C19 | rs12248560 | T | -806C > T, *17 | 0.15 | 0.09 | 0.27 | NA | NA | 0.21 | 0.02 | NA | 0.15 | |
| CYP2C19 | rs4244285 | A | 681G > A, *2 | 0.22 | 0.2 | 0.16 | NA | NA | 0.15 | 0.26 | 0.16 | 0.17 | |
| CYP2D6 | rs3892097 | A | 1846G > A, *4 | 0.0 | 0.01 | NA | NA | NA | 0.5 | NA | NA | NA | |
| CYP3A4 | rs4986910 | C | 1334T > C;M445T, *3 | 0.0 | 0.0 | 0.0 | NA | NA | 0.0 | 0.0 | 0.0 | 0.03 | |
| CYP3A4 | rs4986909 | T | 1247C > T; P416L, *13 | 0.0 | 0.0 | 0.0 | NA | NA | 0.0 | 0.0 | NA | NA | |
| CYP3A4 | rs28371759 | C | 878T > C; L293P, *18 | 0.0 | 0.0 | NA | NA | NA | NA | NA | NA | NA | |
| CYP3A4 | rs4986907 | A | 485G > A; R162Q, *15A | 0.01 | 0.0 | 0.0 | NA | NA | 0.0 | 0.0 | 0.0 | 0.03 | |
| CYP3A4 | rs4987161 | C | 566T > C; F189S, *17 | 0.0 | 0.0 | 0.0 | NA | NA | 0.0 | 0.0 | NA | NA | |
| CYP3A4 | rs2740574 | G | -392A > G, *1B | 0.77 | 0.58 | 0.75 | NA | NA | 0.03 | 0.0 | 0.11 | 0.68 | |
| CYP3A5 | rs4646450 | T | -1630 T > C | 0.97 | 0.83 | 1.0 | 0.98 | 0.85 | 0.13 | 0.34 | NA | NA | |
| CYP3A5 | rs10264272 | A | 711G > A;K208K, *6 | 0.2 | 0.17 | 0.15 | 0.25 | 0.14 | 0.0 | 0.0 | 0.02 | 0.11 | |
| CYP3A7 | rs10211 | G | 129 A > G | 0.35 | 0.52 | 0.75 | 0.72 | 0.44 | 0.06 | 0.34 | 0.19 | 0.58 | |
| Phase II | UGT1A1 | rs4148323 | A | 211G > A;G71R, *6 | 0.0 | 0.0 | 0.0 | NA | NA | 0.0 | 0.2 | 0.03 | 0.0 |
| UGT1A1 | rs887829 | T | 601324 C > T | 0.35 | 0.36 | 0.55 | NA | NA | 0.28 | 0.08 | 0.35 | 0.57 | |
| UGT1A1 | rs10929302 | A | 598536 G > A, *93 | 0.25 | 0.29 | 0.36 | NA | NA | 0.26 | 0.08 | NA | NA | |
MAF data for non-South African populations were obtained from the National Center for Biotechnology Information (NCBI) dbSNP database (http://www.ncbi.nlm.nih.gov/projects/SNP)
Abbreviations: AA, amino acid; AAm, African American; N = total number of samples per population; NA, no data available in the NCBI dbSNP database; NTpos, nucleotide position; Phase I, Phase I drug metabolising enzymes; Phase II, Phase II I drug metabolising enzymes; CMA, Cape Mixed Ancestry; MAF, minor allele frequency
N.B. HapMap Caucasian minor alleles and MAFs are used as the reference in this table.