Refers to the word what but used when a situation turns awkward or weird, when you just can't understand what's going on. More likely to be typed , but wut is also said by different ways like "whut" or "woot".
Jack: bro, u remember that girl in the bar, last saturday ?
Andrew: yeah, the blonde one ? the one you got kissed by ?
Jack : exactly. well she was in fact my cousin lmao
Andrew: wait wut