Table 3.
The annotation information for clinically important variants that GATK HC found, but VarScan and MuTect2 were never found.
| Symbol | Existing_variation | Consequence | SIFT | PolyPhen | CADD | ClinVar annotations |
|---|---|---|---|---|---|---|
| ABCA4 | rs61750130 | Missense_variant | 0 | 0.716 | 28.1 | Pathogenic, risk factor |
| ABCA4 | rs140482171 | Missense_variant | 0.16 | 0.013 | 21.7 | Likely pathogenic |
| DHCR7 | rs11555217 | Stop_gained | 36 | Pathogenic | ||
| ABCA4 | rs1801581 | Missense_variant | 0.01 | 0.163 | 22.7 | Pathogenic, risk factor |
| CYP4V2 | rs199476189 | Stop_gained | <NA> | <NA> | 42 | Pathogenic |
| CFTR | rs121909021 | Missense_variant | 0.02 | 0.531 | 27.5 | Pathogenic |
| CFTR | rs78655421 | Missense_variant | 0 | 1 | 24.9 | Pathogenic, drug response |