Table 2.
Counts of Ensembl consequence type for variants mapped to canonical transcripts of PGRNseq captured genes
| ENSEMBL consequence type | IN PGx | IN 1KG | IN EXAC | NOVEL |
|---|---|---|---|---|
| Upstream Gene Variant | 6,094 | 2,122 | 23 | 3,924 |
| Intron Variant | 5,542 | 2,016 | 460 | 3,038 |
| Missense Variant | 4,806 | 1,485 | 1,792 | 2,212 |
| 3 Prime UTR Variant | 4,245 | 1,539 | 65 | 2,629 |
| Downstream Gene Variant | 3,574 | 1,239 | 44 | 2,219 |
| Synonymous Variant | 3,147 | 1,335 | 1,255 | 1,163 |
| 5 Prime UTR Variant | 931 | 287 | 59 | 597 |
| Missense Variant, Splice Region Variant | 147 | 48 | 62 | 60 |
| Splice Region Variant, Intron Variant | 142 | 60 | 49 | 54 |
| Stop Gained | 97 | 20 | 31 | 54 |
| Splice Region Variant, Synonymous Variant | 90 | — | 36 | 40 |
| Splice Acceptor Variant | 18 | 5 | 3 | 1 2 |
| Splice Donor Variant | 15 | 3 | 6 | 8 |
| Splice Region Variant, 5 Prime UTR Variant | 14 | 3 | 3 | 10 |
| Initiator Codon Variant | 11 | 2 | 2 | 7 |
| Stop Gained, Splice Region Variant | 3 | 1 | 1 | 2 |
| Stop Lost | 2 | — | — | 2 |
| Stop Retained Variant | 1 | 1 | — | — |
| Splice Region Variant, 3 Prime UTR Variant | 1 | 1 | — | — |
| Total | 28,880 | 10,167 | 3,891 | 16,019 |
Counts of variants previously discovered in the 1000 Genomes Project (1KG), the Exome Aggregation Consortium (EXAC), and novel variants in the eMERGE PGx project (PGx) are also shown.