We found significant enrichment of biallelic MCM9 variants in individuals with colonic polyps (odds ratio [OR] 6.51, 95% confidence interval [CI] 1.24–34.11, p = 0.03), rectal polyps (OR 8.40, 95% CI 1.28–55.35, p = 0.03), and gastric cancer (OR 27.03, 95% CI 2.93–248.5; p = 0.004) in data from the 100000 Genomes Project, compared to controls. This evidence concerns the gene MCM9 and colon inflammatory polyp.