Which database would you like to choose to filter those common SNPs and find out rare ones which may be disease-causing? I used to apply 1000Genome as well as ESP (exome sequencing project) database. (ESP is derived from exome data of about 6500 individuals, which is fairly large enough.) Also both databases contains MAF. I don't initially use dbSNP, because it simply contains everything thus less permissive.
But I find sth. interesting today that, there are some SNPs, for example rs73979896: http://genome.ucsc.edu/cgi-bin/hgc?hgsid=308088757&c=chr17&o=21319207&t=21319208&g=snp135Common&i=rs73979896
THis SNP, nonsynonymous, present in dbSNP-135, with a very high MAF=49% derived from around 2204 alleles; however, it's absent from either 1000Genome (2012-Apr) or ESP-6500 (The latest version with exome data from 6500 individuals)! If this is really a true SNP with MAF=49%, how can it NOT be captured in ESP with information of 6500 ppl? This is very confusing.