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Table 1 Observed coding and intronic sequence variants and genotype frequencies in familial breast cancer cases

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

SNP Designation    Genotype Frequency  
SNP SNP ID1 dbSNP ID Amino acid change Location Common homozygote (expected)2 Heterozygote (expected)2 Rare homozygote (expected)2 MAF
1 c.160-179deIT N/A - Intron 1 0.94 (0.91) 0.02 (0.09) 0.04 (0.00) 0.046
2 c.60-51A>T N/A - Intron 1 0.81 (0.82) 0.19 (0.17) 0.00 (0.01) 0.093
3 c. 293-43G>A N/A - Intron 3 0.94 (0.90) 0.02 (0.10) 0.04 (0.00) 0.049
4 c. 293-19C>T N/A - Intron 3 0.94 (0.94) 0.06 (0.06) 0.00 (0.00) 0.029
5* c.632C>T rs2227928 Thr211Met Exon 4 0.42 (0.38) 0.38 (0.47) 0.19 (0.15) 0.385
6 c. 946G>A rs28897764 Va131611e Exon 4 0.94 (0.90) 0.02 (0.10) 0.04 (0.00) 0.047
7 c. 1326A>G rs28897765 Lys442Lys Exon 5 0.94 (0.91) 0.02 (0.09) 0.04 (0.00) 0.046
8 c. 1488C>T N/A Val496Val Exon 6 0.98 (0.98) 0.02 (0.02) 0.00 (0.00) 0.010
9 c. 1732+I66A>G N/A - Intron 7 0.98 (0.98) 0.02 (0.02) 0.00 (0.00) 0.009
10 c. 1732+279A>G N/A - Intorn 7 0.94 (0.94) 0.06 (0.06) 0.00 (0.00) 0.028
11 c. 1776A>T rs2227930 Gly592Gly Exon 8 0.40 (0.34) 0.38 (0.49) 0.23 (0.17) 0.415
12 c. 1815T>C rs2227929 Asp605Asp Exon 8 0.40 (0.35) 0.40 (0.48) 0.21 (0.17) 0.406
13 c. 1950G>A rs28910270 Glu650Glu Exon 9 0.94 (0.91) 0.02 (0.09) 0.04 (0.00) 0.047
14 c.2290A>G N/A Lys764Glu Exon 10 0.98 (0.98) 0.02 (0.10) 0.00 (0.00) 0.010
15 c. 2634-74T>C rs9869842 - Inton 12 0.39 (0.34) 0.39 (0.49) 0.22 (0.17) 0.417
16 c. 2875G>A rs28910271 Val959Met Exon 14 0.94 (0.90) 0.02 (0.10) 0.04 (0.00) 0.052
17 c. 2977-97T>C N/A - Intron 14 0.94 (0.91) 0.02 (0.09) 0.04 (0.00) 0.048
18 c. 3120G>A rs28910272 Leu1040Leu Exon 15 0.94 (0.91) 0.02 (0.09) 0.04 (0.00) 0.048
19 c.3172-26T>A N/A - Intron 15 0.94 (0.91) 0.02 10.09) 0.04 (0.00) 0.046
20 c.3357+128G>A rs13091637 - Intron 16 0.50 (0.51) 0.43 (0.41) 0.07 (0.08) 0.287
21 c. 3725+51T>G N/A - Intron 19 0.98 (0.98) 0.02 (0.02) 0.00 (0.00) 0.009
22 c. 3726-47A>G N/A - Intron 19 0.76 (0.74) 0.20 (0.24) 0.04 (0.02) 0.139
23 c.3945+171C>T N/A - Intron 21 0.96 (0.93) 0.00 (0.07) 0.04 (0.00) 0.038
24 c. 3946-48C>A N/A - Intron 21 0.94 (0.91) 0.02 (0.09) 0.04 (0.00) 0.046
25 c. 4383-232T>G rs9855919 - Intron 24 0.43 (0.38) 0.36 (0.47) 0.21 (0.15) 0.387
26 c.4383-177C>T rs10804682 - Intron 24 0.72 (0.74) 0.28 (0.24) 0.00 (0.02) 0.139
27 c. 5208T>C rs2227931 Tyr1736Tyr Exon 30 0.38 (0.32) 0.37 (0.49) 0.25 (0.19) 0.441
28 c. 5288+130G>A rs11916455 - Intron 30 0.44 (0.26) 0.31 (0.48) 0.25 (0.16) 0.403
29 c. 5380+121C>A rs11927681 - Intron 31 0.87 (0.87) 0.13 (0.13) 0.00 (0.00) 0.065
30 c. 5460T>C rs2227932 Tyr1820Tyr Exon 32 0.79 (0.78) 0.19 (0.21) 0.02 (0.01) 0.115
31 c. 5558+119C>T N/A - Intron 32 0.96 (0.92) 0.00 (0.08) 0.04 (0.00) 0.038
32 c. 5739-4dc19+T N/A - Intron 33 0.94 (0.91) 0.02 (0.09) 0.04 (0.00) 0.046
33 c.5868C>T N/A Tyr1956Tyr Exon 34 0.96 (0.93) 0.00 (0.07) 0.04 (0.00) 0.038
34 c. 6394T>G rs28910273 Tyr2132Asp Exon 38 0.98 (0.98) 0.02 (0.02) 0.00 (0.00) 0.009
35 c. 6553-45C>G N/A - Intron 38 0.98 (0.98) 0.02 (0.02) 0.00 (0.00) 0.010
36 c. 6897+88A>G N/A - Intron 40 0 98 (0 98) 0.02 (0.02) 0.00 (0.00) 0.009
37 c. 7041+8G>A N/A - Intron 41 0.98 (0.98) 0.02 (0.02) 0.00 (0.00) 0.009
38 c. 7041+55T>A N/A - Intron 41 0.98 (0.98) 0.02 (0.02) 0.00 (0.00) 0.009
39 c. 7274G>A rs2229032 Arg2425Gln Exon 43 0.75 (0.73) 0.02 (0.25) 0.04 (0.02) 0.147
40 c. 7875A>G rs1802904 Gln2625Gln Exon 47 0.80 (0.77) 0.16 (0.22) 0.04 (0.01) 0.120
41 c. 7932+104T>C rs10935463 - Intron 47 0.39 (0.33) 0.37 (0.49) 0.24 (0.18) 0.422
  1. 1According to the nomenclature of the Human Genome Variation Society
  2. 2As expected under Hardy-Weinberg equilibrium
  3. N/A: Information not available for this SNP (not reported in dbSNP)
  4. T allele is considered as the common allele according to the reference sequence NM_001184
  5. MAF : Minor Allele Frequency