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Table 4 Variant annotation

From: Incidental germline findings during molecular profiling of tumor tissues for precision oncology: molecular survey and methodological obstacles

  Manual assignment ISOWN assignment
Germline Somatic Variants of uncertain origin Germline Somatic
Total ISOWN: germline ISOWN: somatic
Total 478 920 133 87 46 701 830
Annotated in COSMIC 151 (31.6%) 329 (35.8%) 34 (25.6%) 20 (23.0%) 14 (30.4%) 204 (29.1%) 310 (37.3%)
Annotated in dbSNP 423 (88.5%) 331 (36.0%) 82 (61.7%) 66 (75.9%) 16 (34.8%) 547 (78.0%) 289 (34.8%)
VAF (mean ± SD) 52% ± 15% 28% ± 21% 48% ± 16% 48% ± 17% 48% ± 14% 47% ± 20% 29% ± 20%
Minimal hotspot VAF (mean ± SD) 19% ± 19% 17% ± 19% 22% ± 18% 23% ± 17% 20% ± 18% 20% ± 20% 16% ± 17%
Maximal hotspot VAF (mean ± SD) 49% ± 29% 49% ± 28% 53% ± 27% 56% ± 27% 49% ± 27% 47% ± 30% 49% ± 28%
Maximal hotspot VAF—current (mean ± SD) − 7.6% ± 32% 21% ± 31% 5.2% ± 28% 8.0% ± 28% − 0.06% ± 26% 0.09% ± 34% 19% ± 31%
Maximal hotspot VAF—minimal hotspot VAF (mean ± SD) 26% ± 25% 31% ± 25% 31% ± 25% 33% ± 25% 28% ± 25% 27% ± 26% 32% ± 25%
EXAC frequency (mean) 1.28% 0.0017% 0.004% 0.005% 0.002% 0.88% 0.0013%
TOPMED frequency (mean) 1.23% 0.0012% 0.0026% 0.0029% 0.002% 0.84% 0.0013%
1000G frequency (mean) 1.16% 0.0015% 0.0038% 0.0037% 0.0039% 0.79% 0.0014%