significant SNPs from per-phenotype GWAS summary statistics

Question

[Jennifer]

I performed an analysis for a specific gene/region of interest using GWAS summary statistics for a binary phenotype (+/- disease). Using the corrected p values in the summary statistics and mapping in FUMA, I found a significant missense/coding SNP, with p=0.025. Other papers have shown this SNP leads to a less functional protein. This SNP was not in LD with the other sig SNPs (intronic/non-coding). Could it be an independent SNP? Beta is 0.002 and MAF is 0.005. Is it possible this SNP is a false positive due to its rarity? Population size is n=400k and cases n=1100. Any help would be appreciated!