I need help

So according to this app I was supposed to get my period today. I didn't. And ever since yesterday I've had pains at night time that are not period cramps, they're more in the middle of my torso if that makes sense. What could this mean?? I'm freaking out a little because I'm only 16 and if I'm possibly pregnant my dad will kill me. Yes I used protection if I had sex. Sometimes it was protected but nothing happened. Help please and thank you xoxo