Possibly pregnant?? I need advice!

The start of my cycle was March 11, 56 days ago. My boyfriend and I have had sex multiple times between this time. I've been so busy with school that I didn't even notice that I missed my period. I didn't think anything of it until I had very light brown discharge for about 4-5 days. I had looked up what brown discharge means and read that it would happen early pregnancy during the time your period would normally be. I went into my Fitbit app and realized that this brown discharge was the same time as my predicted period. I've been having mild headaches, fatigue (like extremely tired), and peeing frequently. I haven't had overwhelming nausea but I have had some to the point where I don't want to eat a whole lot or can't eat a normal sized meal. I took a clear blue pregnancy test this morning but it said not pregnant. I'm so confused on why my period is so late and I'm having some symptoms but even then, I'm not sure! My boyfriend and I were kind of worried at first but we have been together for 5 years and got excited after talking about it more. Could someone help and possibly give some advice? I'm not sure what to do at this point.