In this study of 41 non-synonymous coding SNPs, selected based on prior evidence of association with breast cancer, we have identified a novel susceptibility locus at 3p21 based on SNP rs1053338 (K264R) in ATXN7. We have also confirmed for the first time at genome-wide statistical significance, that AKAP9-rs6964587 (M463I) at 7q21 is a marker of breast cancer susceptibility in European women. This evidence concerns the gene AKAP9 and breast carcinoma.