Due to very low frequency of such SNP, they have no use in GWAS as if one SNP (AA) is present 99 time and other one just once (BB) but significantly associating, mean SNP variant is very less prevalent and we can not say with assurance that the significant SNP variants are completely responsible for the associated traits. So, just we remove such type of SNP from our study. Its my view, might be something other reason there.