Table 4.

Relationship between functionality of nsSNPs predicted by Grantham, PolyPhen, and SIFT and MAF based on dbSNP Population 1371 (Perlegen European Americans)

Grantham prediction
ConservativeModerately conservativeModerately radicalRadicalTotal
MAF
    ≤0.0584 (7.7)82 (7.5)20 (1.8)13 (1.2)199 (18.3)
    0.051-0.15145 (13.3)123 (11.3)24 (2.2)13 (1.2)305 (28.0)
    0.151-0.30133 (12.2)124 (11.4)21 (1.9)11 (1.0)289 (26.5)
    >0.30145 (13.3)112 (10.3)29 (2.8)11 (1.0)297 (27.3)
    Total507 (46.5)441 (40.5)94 (8.6)48 (4.4)1,090
ρ = −0.035; 95% CI: −0.094, 0.025
PolyPhen prediction

Benign
Borderline
Potentially damaging
Possibly damaging
Probably damaging
Total
MAF
    ≤0.0559 (7.8)15 (2.0)19 (2.5)28 (3.7)22 (2.9)143 (18.9)
    0.051-0.1599 (13.1)20 (2.6)34 (4.5)43 (5.7)25 (3.3)221 (29.2)
    0.151-0.3087 (11.5)27 (3.6)23 (3.0)31 (4.1)12 (1.6)180 (23.8)
    >0.30114 (15.1)22 (2.9)32 (4.2)24 (3.2)20 (2.6)212 (28.0)
    Total359 (47.5)84 (11.1)108 (14.3)126 (16.7)79 (10.5)756
ρ = −0.113; 95% CI: −0.183, −0.042
SIFT prediction

Tolerant
Borderline
Potentially intolerant
Intolerant
Total
MAF
    ≤0.0590 (10.6)23 (2.7)14 (1.7)40 (4.7)167 (19.7)
    0.051-0.15153 (18.1)26 (3.1)18 (2.1)52 (6.1)249 (29.4)
    0.151-0.30153 (18.1)32 (3.8)18 (2.1)25 (3.0)228 (27.0)
    >0.30143 (16.9)19 (2.2)13 (1.5)27 (3.2)202 (23.9)
    Total539 (63.7)100 (11.8)63 (7.4)144 (17.0)846
ρ = 0.172; 95% CI: 0.105, 0.236
  • NOTE: Percentages are shown in parentheses.