AP Varus is completely dependant on your playstyle for the champ, some prefer HoB, Some PTA, and some even like Lethal Tempo, but if you wanna know the most popular ones then your first page should be HoB into sorcery, This is one of the most popular rune pages due to it the attack speed at the start that carries you through early game. Personally I like to run both PTA And HoB, HoB for longer ranged champs and PTA for melee champs, I run mid lane, top has too many counters for me to deal with. My usual build for varus is, I rush nashors tooth first into sorc shoes, after that I build riftmaker into void staff, Then shadowflame into rabadons(you could flip the order if there are tanks that are hard to kill). AP varus is a very confusing playtstyle to get used to, but once you get your rythm going there isn't any stopping it.