Table 4.
Comparison of study variant MAF to online database variant MAF for highly discordant positions and Hardy-Weinberg equilibrium tests
| Approach | Chr19 Position (GRCh37) | rsid | Ref>Var | Gene | Error Type | Ancestry | A1 HWE p-valuec |
Discordant Approach HWE p-valuec | Study MAFa | ALFA MAFa | 1000G MAFa | gnomAD MAFa,b |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| A2+A4 | 41349750 | rs5031017 | C>A | CYP2A6 | FP | AFR | 1 | 0.23 (A2)/ 0.30 (A4) |
0 | 0.0012 | na | 0.00018 |
| A3 | 41354533 | rs1801272 | A>T | CYP2A6 | Mostly FP | EUR | 1 | 0.08 | 0.024 | 0.026 | 0.034 | 0.027 |
| A5 | 41350648 | rs28399461 | A>G | CYP2A6 | Mostly FN | AFR | 0.28 | 0.79 | 0.15 | 0.12 | 0.15 | 0.13 |
| A5 | 41350582 | rs8192730 | C>G | CYP2A6 | Mostly FP | AFR | 1 | 0.0028 | 0.016 | 0.016 | na | 0.0099 |
| A5 | 41350587 | rs28399463 | T>C | CYP2A6 | Mostly FP | AFR | 1 | 0.0033 | 0.019 | 0.017 | 0.026 | 0.012 |
| A5 | 41350594 | rs2002977 | G>A | CYP2A6 | FP | AFR | 0.82 | 7.3×10 −7 | 0.11 | 0.094 | 0.11 | 0.093 |
| A5 | 41387620 | rs10425150 | A>G | CYP2A7 | Mostly FP | AFR | 0.93 | 0.60 | 0.43 | 0.21 | 0.43 | 0.41 |
| A5 | 41387647 | rs10425169 | A>G | CYP2A7 | Mostly FP | AFR | 0.86 | 0.97 | 0.43 | 0.44 | 0.43 | 0.32 |
| A5 | 41387656 | rs10425176 | A>T | CYP2A7 | Mostly FP | AFR | 1 | 0.57 | 0.44 | 0.44 | 0.42 | 0.33 |
| A6 | 41349786 | rs145014075 | G>T | CYP2A6 | FP | AFR | N/Ad | 1 | 0 | 0.011 | na | 0.028 |
| A6 | 41349874 | rs143731390 | T>A | CYP2A6 | FP | EUR | 1 | 0.14 | 0 | 0.031 | na | na |
| A6 | 41352807 | rs55805386 | A>C | CYP2A6 | FP | EUR | 1 | 0.38 | 0.0011 | 0.018 | na | na |
| A6 | 41355849 | rs2302990 | A>G | CYP2A6 | FP | EUR | 1 | 6.0×10 −4 | 0 | 0.010 | na | na |
| AFR | 1 | 0.0027 | 0.0010 | 0.0038 | na | na | ||||||
| A6 | 41515192 | rs376359134 | G>A | CYP2B6 | FN | EUR | 7.5×10 −21 | 1 | 0.20 | 0.013 | na | 0.0016 |
| AFR | 1.7×10 −4 | 1 | 0.13 | 0.0038 | na | 0.0017 | ||||||
| A6 | 41515263 | rs2279343 | A>G | CYP2B6 | FN | EUR | 9.8×10 −27 | 1 | 0.36 | 0.23 | na | 0.086 |
a.
MAFs for EUR or AFR according to the “Ancestry” column
b.
Using the gnomAD Exomes dataset
c.
Variants differing significantly (p<0.05) from HWE are bolded
d.
HWE testing was not possible due to MAF=0
1000G: 1000 Genomes Project; AFR: African-ancestry individuals; EUR: European-ancestry individuals; FN: False Negative; FP: False positive; MAF: Minor allele frequency