Time to rewatch the season and look for hints guys. Off the top of my head, would the fact that she didn't give nudes to Tommy a hint she might be trans*? Also, I think on a highschool relationship timeline, when she broke up with Tommy would be about the time he would want sex, in which case she would be forced to tell him. Or maybe it's HIV?
Edit: Her ex friends commented how she has her period every two weeks and irregular/more frequent periods can be a symptom of HIV. Although that comment could have also been a figurative waybto say she gets bitchy all the time.