am i changing cycles or pregnant

So my boyfriend and i have been dating for 1 year and 6 months. We were long distance up until about 2 months ago so we've been having a lot of sex. When we were long distance we would fuck but not that often bc we didnt see each other so much. Anyways, i have never been late for my period. I always get it the last day of the month or the 1st. I am now 2 days late. 
We have sex with a condom on and he pulls out too, just to be extra sure. We always check for broke condoms. We are super careful. But the day before my period was supposed to come he put his dick in me without a condom for like 30 seconds. But apart from that, we have never had unprotected sex. 
I'm 16 almost 17, and been having my period for 5 years. My periods have always been regular so I don't know why this is happening and im really afraid. 
Has this happened to anyone or can anyone help me? 
((Please no negative comments)