Table 3. The number of indels and SNPs by impact group and minor allele frequency (MAF).
| Type | MAF | LoF * (Frameshift indels, splice acceptor/ donor, stop gained/lost, initiator codon) | MODERATE (Inframe indels, missense, splice region) | LOW (Synonymous, stop retained, 3′/5′ UTR) | Other (Intronic, intergenic) | Total |
|---|---|---|---|---|---|---|
| Percentages are for the proportion of variants that fall in each class within the row. | ||||||
| SNP | ≥0.5% | 602 (0.0070%) | 36,282 (0.42%) | 108,850 (1.3%) | 8,445,855 (98.3%) | 8,591,589 |
| 0.1% to 0.5% | 915 (0.023%) | 29,659 (0.76%) | 59,076 (1.5%) | 3,836,528 (97.7%) | 3,926,178 | |
| <0.1% | 2,462 (0.034%) | 57,209 (0.80%) | 101,751 (1.4%) | 7,010,453 (97.7%) | 7,171,875 | |
| All | 3,979 (0.020%) | 123,150 (0.63%) | 269,677 (1.4%) | 19,292,836 (98.0%) | 19,689,642 | |
| Indel | ≥0.5% | 418 (0.0609%) | 797 (0.12%) | 8,352 (1.2%) | 676,820 (98.6%) | 686,387 |
| 0.1% to 0.5% | 677 (0.229%) | 568 (0.19%) | 4,380 (1.5%) | 290,492 (98.1%) | 296,117 | |
| <0.1% | 1,721 (0.375%) | 1,027 (0.22%) | 6,757 (1.5%) | 449,563 (97.9%) | 459,068 | |
| All | 2,816 (0.195%) | 2,392 (0.17%) | 19,489 (1.4%) | 1,416,875 (98.3%) | 1,441,572 |
*Loss of function. Table reproduced from Table 1 of ref. 13.