If the qb is under the center, then it is used to send one of the players in motion, either WR, TE, or RB. If in the shotgun it's used to either send a player in motion, or to signal the center that the are ready for the snap. It's hard to hear the qb if hes 5 yards behind you, and even then he could be audbling and talking to somone else, the easiest way to avoid this confussion is to just look for the leg to go up.