Snap
 

QB fakes taking the direct snap from the center who holds onto the ball and the running back steps up and takes the ball from centers hands and runs for a touchdown. Is the legal?

Depends on the timing and what "fakes taking the direct snap" means.

Pretending to take a snap while the snapper instead leaves the ball in its spotted condition is a false start. So if center "holds onto the ball" by not moving it at all, while QB makes a hand or arm movement that looks like taking the snap, that's a false start.

Also, if the snapper starts the snapping motion but then holds onto the ball by keeping it in one position, then by American rules that's also a false start or illegal snap, although by Canadian rules it's legal. The motion of the ball in American rules has to be quick and continuous from the time the snapper starts moving it until he loses contact with it by hand or hands, while in Canadian rules the centre is allowed to keep hold of the ball as long as he eventually gets rid of it after moving it. However, pretending to take the snap while the ball is left unmoved is illegal procedure, but pretending to take the snap as or after the ball has been initially moved is legal, in both American and Canadian rules.

In either American or Canadian rules, any number of players are allowed to fake taking the snap while another player actually gets the snap. It's only in Canadian rules that the snapper is allowed to hesitate with the ball after moving it.

In American rules there may also be a problem with the "running back steps up" bit. If play hasn't already become dead due to a false start, if the back was moving forward ("up"?) or, by stopping in place for less than a second, failed to complete a legal shift, that's an illegal motion or shift.

There are ways you might try making a close substitute for this play that's legal in American rules, but at least one of them has been foreclosed. You might have the snapper snap the ball to the ground just behind him, but NCAA has outlawed such a "planned loose ball in the vicinity of the snapper", and in Fed you have to tell the referee you're going to do it on that play, and he has to tell the other team. What is legal is to have a back crouching low near the snapper to take the snap, which may be hard for the other team to see. It's also legal to have a sleeper play, on which you snap the ball and pretend it hasn't been snapped yet, having the quarterback continue audible signals and the other players freeze as if anticipating the play.

NFHS Snap Infraction- a snap must be a quick and continuous motion and must leave the snapper's hand immediately.