Table 5 Summary of amino acid changes in study cohort, stratified by evidence of clinical implication
| Â | No clinical implication | With clinical implication | Sum | p Value | ||
|---|---|---|---|---|---|---|
N | % | N | % | N | ||
Total | 5 | 2.8% | 171 | 97.2% | 176 | – |
Gene | ||||||
 BRCA1 | 1 | 2.0% | 48 | 98.0% | 49 (27.8%) | 0.415 |
 BRCA2 | 4 | 4.3% | 90 | 95.7% | 94 (53.4%) |  |
 PALB2 | 0 | 0.0% | 33 | 100.0% | 33 (18.8%) |  |
Site | ||||||
 Exonic | 4 | 2.7% | 146 | 97.3% | 150 (85.2%) | 0.738 |
 Splicesite | 1 | 3.8% | 25 | 96.2% | 26 (14.8%) |  |
Type of mutation | ||||||
 Frameshift deletion | 0 | 0.0% | 28 | 100.0% | 28 (15.9%) |  < 0.001 |
 Frameshift insertion | 0 | 0.0% | 52 | 100.0% | 52 (29.5%) |  |
 Missense | 4 | 50.0% | 4 | 50.0% | 8 (4.5%) |  |
 Nonsense | 0 | 0.0% | 62 | 100.0% | 62 (35.2%) |  |
 Unknown | 1 | 3.8% | 25 | 96.2% | 26 (14.8%) |  |
Annotation, by Clinvar | ||||||
 Pathogenic | 0 | 0.0% | 68 | 100.0% | 68 (38.6%) |  < 0.001 |
 Likely Pathogenic | 0 | 0.0% | 5 | 100.0% | 5 (2.8%) |  |
 Pathogenic/Likely Pathogenic | 0 | 0.0% | 6 | 100.0% | 6 (3.4%) |  |
 Conflicting | 2 | 50.0% | 2 | 50.0% | 4 (2.3%) |  |
 Benign | 1 | 100.0% | 0 | 0.0% | 1 (0.6%) |  |
 Uncertain significance | 1 | 33.3% | 2 | 66.7% | 3 (1.7%) |  |
 Unknown | 1 | 1.1% | 88 | 98.9% | 89 (50.6%) |  |
Annotation, by Oncomine | ||||||
 No annotation | 3 | 13.6% | 19 | 86.4% | 22 (12.5%) |  < 0.001 |
 Deleterious | 0 | 0.0% | 142 | 100.0% | 142 (80.7%) |  |
 Hotspot | 2 | 16.7% | 10 | 83.3% | 12 (6.8%) |  |
Annotation, comparing ClinVar to Oncomine | ||||||
 ClinVar(+), Oncomine(+) | 0 | 0.0% | 70 | 100.0% | 70 (39.8%) |  < 0.001 |
 ClinVar(+), Oncomine(−) | 0 | 0.0% | 9 | 100.0% | 9 (5.1%) |  |
 ClinVar(−), Oncomine(+) | 2 | 2.4% | 82 | 97.6% | 84 (47.7%) |  |
 ClinVar(−), Oncomine(−) | 3 | 23.1% | 10 | 76.9% | 13 (7.4%) |  |