There should be no clearance. Ideally the frets and the bridge (not the saddle) should be on the same plane. That way the saddle can give whatever action height is desired. As string tension distorts the instrument over time this plane is altered, sometimes to the point where the neck has to be reset to reestablish the frets/bridge relationship to lower the action again. Too often the bridge/saddle is reduced in height instead, and while this lowers the action it usually handicaps the performance of the instrument.