Table 7.
Assessment of the lung cancer dataset (100 patients) by VIC, ClinVar, SIFT, PolyPhen-2, and COSMIC. The number of reported variants with strong or potential clinical significance from the diagnostic lab is also listed
| VIC | |||||
|---|---|---|---|---|---|
| Strong | Potential | Uncertain | Benign/likely benign | Total | |
| ClinVar | |||||
| Pathogenic | 27 | 58 | 3 | 0 | 88 |
| Conflict | 0 | 0 | 0 | 0 | 0 |
| Benign | 0 | 0 | 0 | 0 | 0 |
| Uncertain | 0 | 1 | 0 | 0 | 1 |
| Other | 0 | 1 | 0 | 0 | 1 |
| N/A | 0 | 1 | 5 | 0 | 6 |
| SIFT | |||||
| Damaging | 27 | 40 | 0 | 0 | 67 |
| Benign | 0 | 1 | 1 | 0 | 2 |
| N/A | 0 | 20 | 7 | 0 | 27 |
| PolyPhen-2 | |||||
| Damaging | 27 | 33 | 1 | 0 | 61 |
| Benign | 0 | 8 | 0 | 0 | 8 |
| N/A | 0 | 20 | 7 | 0 | 27 |
| COSMIC | |||||
| Pathogenic | 27 | 37 | 1 | 0 | 65 |
| Neutral | 0 | 0 | 0 | 0 | 0 |
| None | 0 | 24 | 5 | 0 | 29 |
| N/A | 0 | 0 | 2 | 0 | 2 |
| VIC | |||||
| Total | 27 | 61 | 8 | 0 | 96 |
N/A no information/not archived, None COSMIC variants without “FATHMM_prediction” records in the database