Base editors that direct deaminases to specific genome sites via CRISPR-system enzymes have gained recent attention due to precision base editing without induction of DNA double-strand breaks. However, potential off-target effects on both DNA and RNA may complicate biotechnological and therapeutic applications. To obtain cytosine base editors (CBEs) with increased specificity, Zuo et al. constructed variants of rAPOBEC1, a widely used cytidine deaminase component in CBE, within regions related to DNA and RNA editing activity. Four variants with single or double mutations near putative DNA-binding sites and/or hydrophobic sites required for RNA binding exhibited decreased DNA and RNA off-target effects in embryos and HEK293T cells, yet maintained on-target editing activity. Interestingly, the on-target activity of the variants could be further enhanced by addition of an N-terminal nuclear localization signal and codon optimization. The resulting optimized variant YE1-BE3-FNLS had on-target editing activity comparable to that of the current best base editors, with a nearly basal level of off-target edits. This study demonstrates the use of rational design to improve the performance of base editors for further applications.