Table 3 Call rates on reference genome NA12878, a healthy individual. Although the number of damaging coding and non-coding variants in a healthy individual’s genome is still unknown, presumably damaging variants comprise a low percentage of the total. Relative percentages are shown in the top panel, absolute numbers are shown in the bottom. Rare variants denotes variants with gnomAD population frequencies < 1/1000
From: The VAAST Variant Prioritizer (VVP): ultrafast, easy to use whole genome variant prioritization tool
All Variants (%) | Rare Variants (%) | |||||
CODING | VVP | CADD | SIFT | VVP | CADD | SIFT |
Pathogenic | 4.0 | 11.1 | 13.2 | 23.5 | 31.7 | 24.5 |
Benign | 96.0 | 88.9 | 58.1 | 76.5 | 68.6 | 56.9 |
Not Scored | 0.0 | 0.0 | 28.7 | 0 | 0.0 | 18.6 |
NON-CODING | VVP | CADD | SIFT | VVP | CADD | SIFT |
Pathogenic | 1.7 | 3.5 | 0 | 43.23 | 4.33 | 0 |
Benign | 98.3 | 96.5 | 0 | 56.77 | 95.67 | 0 |
Not Scored | 0 | 0 | 100 | 0 | 0 | 100 |
All Variants (variants) | Rare Variants (variants) | |||||
CODING | VVP | CADD | SIFT | VVP | CADD | SIFT |
Pathogenic | 577 | 1577 | 1883 | 48 | 64 | 50 |
Benign | 13,710 | 12,710 | 8304 | 156 | 140 | 116 |
Not Scored | 0.0 | 0.0 | 4100 | 0 | 0.0 | 38 |
NON-CODING | VVP | CADD | SIFT | VVP | CADD | SIFT |
Pathogenic | 31,079 | 64,571 | 0 | 3769 | 378 | 0 |
Benign | 1,825,253 | 1,791,761 | 0 | 4949 | 8340 | 0 |
Not Scored | 0 | 0 | 1,856,322 | 0 | 0 | 8718 |