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Table 15 Step 4. Effect rs12144939 is removed:

From: Clinical validation of a genetic model to estimate the risk of developing choroidal neovascular age-related macular degeneration

Model convergence status
Convergence criterion (GCONV = 1E-8) satisfied.
Model fit statistics
Criterion Intercept only Intercept and covariates  
AIC 1317.356 1010.903  
SC 1322.212 1059.457  
-2 Log L 1315.356 990.903  
Testing global null hypothesis: BETA = 0
Test Chi-square DF Pr > ChiSq  
Likelihood ratio 324.4536 9 <0.0001  
Score 279.2738 9 <0.0001  
Wald 209.2428 9 <0.0001  
Residual Chi-square test    
Chi-square DF Pr > ChiSq  
2.6773 4 0.6132  
Note: No (additional) effects met the 0.05 significance level for removal from the model.
Summary of backward elimination
Step Effect removed DF Number in Wald Chi-square Pr > ChiSq  
1 rs698859 1 12 0.0031 0.9559  
2 rs1409153 1 11 0.3356 0.5624  
3 rs1750311 1 10 0.3820 0.5366  
4 rs12144939 1 9 1.9468 0.1629  
Analysis of maximum likelihood estimates
Parameter DF Estimate Standard error Wald Chi-square Pr > ChiSq  
Intercept 1 -0.7554 0.2621 8.3051 0.0040  
rs10490924 1 -1.4417 0.1245 134.0342 <0.0001  
rs1061170 1 0.7697 0.2988 6.6352 0.0100  
rs10922153 1 0.7240 0.1950 13.7839 0.0002  
rs2230199 1 -0.4292 0.1286 11.1389 0.0008  
rs2274700 1 0.8593 0.1695 25.7009 <0.0001  
rs2990510 1 0.4556 0.1586 8.2557 0.0041  
rs403846 1 -0.6775 0.3341 4.1118 0.0426  
rs641153 1 0.8243 0.1999 17.0040 <0.0001  
rs9332739 1 0.9509 0.3163 9.0360 0.0026  
Odds ratio estimates
Effect Point estimate 95% Wald confidence limits  
rs10490924 0.237 0.185 0.302  
rs1061170 2.159 1.202 3.878  
rs10922153 2.063 1.407 3.023  
rs2230199 0.651 0.506 0.838  
rs2274700 2.362 1.694 3.292  
rs2990510 1.577 1.156 2.152  
rs403846 0.508 0.264 0.978  
rs641153 2.280 1.541 3.374  
rs9332739 2.588 1.392 4.811  
Association of predicted probabilities and observed responses
Percentage concordant 81.5 Somers' D 0.637  
Percentage discordant 17.9 Gamma 0.641  
Percentage tied 0.6 Tau-a 0.319  
Pairs 225094 c 0.818  
Classification table        
  Correct Incorrect    Percentages   
Prob.
Level
Event Non-
event
Event Non-
event
Correct Sensitivity Specificity False
positive
False
negative
0.000 467 0 482 0 49.2 100.0 0.0 50.8 --
0.020 467 3 479 0 49.5 100.0 0.6 50.6 0.0
0.040 467 20 462 0 51.3 100.0 4.1 49.7 0.0
0.060 467 35 447 0 52.9 100.0 7.3 48.9 0.0
0.080 467 49 433 0 54.4 100.0 10.2 48.1 0.0
0.100 465 65 417 2 55.8 99.6 13.5 47.3 3.0
0.120 461 91 391 6 58.2 98.7 18.9 45.9 6.2
0.140 457 113 369 10 60.1 97.9 23.4 44.7 8.1
0.160 450 143 339 17 62.5 96.4 29.7 43.0 10.6
0.180 448 159 323 19 64.0 95.9 33.0 41.9 10.7
0.200 442 182 300 25 65.8 94.6 37.8 40.4 12.1
0.220 438 200 282 29 67.2 93.8 41.5 39.2 12.7
0.240 435 213 269 32 68.3 93.1 44.2 38.2 13.1
0.260 434 217 265 33 68.6 92.9 45.0 37.9 13.2
0.280 423 227 255 44 68.5 90.6 47.1 37.6 16.2
0.300 422 246 236 45 70.4 90.4 51.0 35.9 15.5
0.320 419 252 230 48 70.7 89.7 52.3 35.4 16.0
0.340 414 271 211 53 72.2 88.7 56.2 33.8 16.4
0.360 410 274 208 57 72.1 87.8 56.8 33.7 17.2
0.380 389 287 195 78 71.2 83.3 59.5 33.4 21.4
0.400 385 303 179 82 72.5 82.4 62.9 31.7 21.3
0.420 381 312 170 86 73.0 81.6 64.7 30.9 21.6
0.440 365 326 156 102 72.8 78.2 67.6 29.9 23.8
0.460 361 331 151 106 72.9 77.3 68.7 29.5 24.3
0.480 358 340 142 109 73.6 76.7 70.5 28.4 24.3
0.500 344 354 128 123 73.6 73.7 73.4 27.1 25.8
0.520 332 357 125 135 72.6 71.1 74.1 27.4 27.4
0.540 324 366 116 143 72.7 69.4 75.9 26.4 28.1
0.560 315 378 104 152 73.0 67.5 78.4 24.8 28.7
0.580 300 389 93 167 72.6 64.2 80.7 23.7 30.0
0.600 293 392 90 174 72.2 62.7 81.3 23.5 30.7
0.620 284 398 84 183 71.9 60.8 82.6 22.8 31.5
0.640 266 410 72 201 71.2 57.0 85.1 21.3 32.9
0.660 252 417 65 215 70.5 54.0 86.5 20.5 34.0
0.680 236 423 59 231 69.4 50.5 87.8 20.0 35.3
0.700 233 427 55 234 69.5 49.9 88.6 19.1 35.4
0.720 196 440 42 271 67.0 42.0 91.3 17.6 38.1
0.740 190 441 41 277 66.5 40.7 91.5 17.7 38.6
0.760 179 448 34 288 66.1 38.3 92.9 16.0 39.1
0.780 170 453 29 297 65.6 36.4 94.0 14.6 39.6
0.800 127 456 26 340 61.4 27.2 94.6 17.0 42.7
0.820 114 467 15 353 61.2 24.4 96.9 11.6 43.0
0.840 103 467 15 364 60.1 22.1 96.9 12.7 43.8
0.860 77 470 12 390 57.6 16.5 97.5 13.5 45.3
0.880 65 471 11 402 56.5 13.9 97.7 14.5 46.0
0.900 53 475 7 414 55.6 11.3 98.5 11.7 46.6
0.920 40 479 3 427 54.7 8.6 99.4 7.0 47.1
0.940 16 481 1 451 52.4 3.4 99.8 5.9 48.4
0.960 9 481 1 458 51.6 1.9 99.8 10.0 48.8
0.980 1 481 1 466 50.8 0.2 99.8 50.0 49.2
1.000 0 482 0 467 50.8 0.0 100.0 -- 49.2