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Table 3 Coding and intronic (MAF>5%) sequence variations and genotype frequencies in familial breast cancer cases and controls

From: Mutation analysis and characterization of ATR sequence variants in breast cancer cases from high-risk French Canadian breast/ovarian cancer families

SNP SNP ID1 Series # individual Common homozygote No. (expected)2 Heterozygote No. (expected)2 Rare homozygote No. (expected)2 MAF3 X2 p-value4
2 c.60-51A>T Cases 54 44 (44.3) 10 (9.2) 0 (0.5) 0.093 0.453
   Controls 62 49 (47.9) 11 (13.2) 2 (0.9) 0.121 0.192
5* c.632C>T Cases 52 22 (19.8) 20 (24,4) 10 (7.8) 0.385 0.176
   Controls 71 26 (29.8) 40 (32.4) 5 (8.8) 0.344 0.048
6 c.946G>A Cases 53 50 (48.1) 1 (4.7) 2 (0.1) 0.047 <0.001
   Controls 68 68 (68.0) 0 (0.0) 0 (0.0) 0.000 -
7 c.1326A>G Cases 54 51 (49.1) 1 (4.9) 2(0.0) 0.046 <0.001
   Controls 72 68 (68.1) 4 (3.9) 0(0.1) 0.028 0.808
8 c.1488C>T Cases 51 50 (50.0) 1 (1.0) 0 (0.0) 0.010 0.944
   Controls 73 73 (73.0) 0 (0.0) 0(0.0) 0.000 -
11 c.1776A>T Cases 53 21 (18.0) 20 (26.0) 12 (9.0) 0.415 0.105
   Controls 70 25 (29.6) 41 (31.8) 4 (8.6) 0.350 0.016
12 c.1815T>C Cases 53 21 (18.5) 21 (25.5) 11 (9.0) 0.406 0.194
   Controls 71 25 (25.5) 35 (34.1) 11 (11.4) 0.401 0.828
13 c.1950G>A Cases 53 50 (48.2) 1 (4.8) 2(0.0) 0.047 <0.001
   Controls 71 68 (68.0) 3 (2.9) 0(0.1) 0.021 0.856
14 c.2290A>G Cases 50 49 (49.0) 1 (1.0) a (0.0) 0.010 0.943
   Controls 72 72 (72.0) 0 (0.0) 0 (0.0) 0.000 -
15 c.2634-74T>C Cases 54 21 (18.3) 21 (26.3) 12 (9.4) 0.417 0.142
   Controls 51 15 (18.2) 31 (24.6) 5 (8.2) 0.402 0.059
16 c.2875G>A Cases 48 4S (43.2) 1 (4.8) 2(0.0) 0.052 <0.001
   Controls 68 64(64.0) 4 (3.9) 0(0.1) 0.028 0.803
18 c.3120G>A Cases 52 49 (47.3) 1 (4.7) 2 (0.0) 0.048 <0.001
   Controls 70 66(66.0) 4 (3.9) 0(0.1) 0.028 0.806
20 c.3357+128G>A Cases 54 27 (27.5) 23(22.1) 4(4.4) 0.287 0.765
   Controls 64 41 (40.7) 20 (20.7) 3 (2.6) 0.203 0.781
22 c.3726-47A>C Cases 54 41 (40.0) 11 (13.0) 2 (1.0) 0.139 0.275
   Controls 65 44(43.2) 18(19.6) 3(2.2) 0.185 0.518
25 c.4383-232T>G Cases 63 33 (19.9) 19 (25.2) 11 (7.9) 0.387 0.013
   Controls 65 23 (25.9) 36 (30.3) 6(8.8) 0.369 0.127
26 c.4383-177C>T Cases 54 39(40.0) 15(13.0) 0(1.0) 0.139 0.236
   Controls 65 37(37.0) 24 (24.1) 4(3.9) 0.246 0.967
27 c.5208T>C Cases 51 39 (16.3) 19 (25.0) 13 (9.7) 0.441 0.081
   Controls 65 23 (23.4) 32 (31.2) 10(10.4) 0.400 0.836
28 c.5288+130G>A Cases 36 16 (12.9) 11 (17.3) 9(5.8) 0.403 0.028
   Controls 55 20 (21.7) 29 (25.7) 6(7.6) 0.372 0.344
29 c.5380+121C>A Cases 46 40 (40.2) 6 (5.6) 0(0.2) 0.065 0.636
   Controls 62 JO (48.8) 10 (12.4) 2 (0.8) 0.113 0.125
30 c.5460T>C Cases 52 41 (40.1) 10(11.4) 1 (0.5) 0.115 0.676
   Controls 72 62 (62.4) 10 (9.3) 0(0.3) 0.069 0.526
32 c.5739-4del9+T Cases 54 51 (49.1) 1 (4.9) 2(0.0) 0.04 <0.001
   Controls 63 60 (60.0) 3 (2.9) 0 (0.0) 0.024 0.846
33 c.5868C>T Cases 53 51 (49.3) 0 (3.7) 2 (0.0) 0.038 <0.001
   Controls 67 67(67.0) 0 (0.0) 0 (0.0) 0.000 -
34 c.6394T>G Cases 54 53 (52.9) 1 (1.1) 0(0.0) 0.009 0.945
   Controls 66 66 (66.0) 0 (0.0) 0 (0.0) 0.000 -
37 c.7041+8G>A Cases 53 52(52.1) 1 (0.9) 0 (0.0) 0.009 0.945
   Controls 70 65 (63.2) 3 (6.6) 2(0.2) 0.050 <0.001
39 c.7274G>A Cases 51 38(37.2) 11 (12.8) 2 (1.0) 0.147 0.317
   Controls 70 39(40.9) 29 (25.2) 2(3.9) 0.236 0.210
40 c.7875A>G Cases 50 40(38.5) 8 (11.0) 2 (0.5) 0.120 0.086
   Controls 63 45 (45.4) 17 (16.1) 1 (1.5) 0.151 0.670
41 c.7932+104T>C Cases 51 20 (17.0) 19 (24.9) 12 (9.1) 0.422 0.009
   Controls 53 19 (18.7) 25 (25.6) 9(8.7) 0.406 0.874
  1. 1 According to the nomenclature of the Human Genome Variation Society
  2. 2 As expected under Hardy-Weinberg equilibrium
  3. 3 Minor allele frequency
  4. 4 p-value for deviation from Hardy-Weinberg equilibrium (Pearson's chi-square)
  5. * T allele is considered as the common allele according to the reference sequence NM_001184