NTHL1 and breast cancer: The association of NTHL1 missense variants with hereditary breast cancer remained when applying a population rarity filter or in silico prediction tools, Condel, PolyPhen2, SIFT, CADD, and REVEL to enrich for likely pathogenic variants, with the strongest effect observed for the missense variants that were selected for rarity (MAF ≤ 0.001, 39 versus 20, OR 1.88, 95% CI: 1.07–3.41) (Supplementary Table 3).