Multiple sequence alignment (MSA) is a fundamental algorithm in bioinformatics, often used to identify structural or functional relationships among sequences. In situations where the alignment must remain confidential while still allowing the verification of other aspects, such as the input sequences and the alignment score, a zero-knowledge proof (ZKP) can be employed. In this setup, a prover generates a cryptographic proof that certain conditions are met, while a validator (or verifier) checks this proof without gaining access to the sensitive alignment data. In this paper, a validator checks the consistency between the input sequence and the alignment, and between the alignment and the alignment score. The validator is written in Circom, a language that compiles into a circuit. Using a zero-knowledge proof system called zkSNARK, a cryptographic proof is generated for the circuit and its inputs, demonstrating that all MSA inputs and outputs are consistent without revealing the actual alignment.