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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