Cook the edamame according to package directions, omitting salt and fat. Cool to room temperature; place in a medium bowl.
Cook haricots verts in boiling water 1 minute or until crisp-tender. Drain and plunge beans into ice water; drain. Add haricots verts, onion, kidney beans, and black beans to edamame.
Combine vinegar and remaining ingredients in a small bowl; stir well with a whisk. Drizzle sake mixture over bean mixture; toss gently to coat. Cover and chill 8 hours or overnight, stirring occasionally. Stir just before serving.