Vat is the indicated airspeed at the threshold which is equal to the stalling speed Vso multiplied by 1.3 or the stalling speed Vs1g multiplied by 1.23. Both Vso and Vs1g apply to aircraft in the landing configuration at maximum certificated landing weight. If both Vso and Vs1g are available for an aircraft, the higher resulting Vat must be used.
Vat is used to categorise aircraft to determine which variation of an instrument approach is used. It seems that the difference is that Vat is calculated at max. landing weight whereas Vref varies with Vso (which varies with weight).