We had intercourse, she is stressed and her period is late

I'm afraid my girlfriend is pregnant. She is about 3 days late but she is an irregular when it comes to periods. We've only had sex 2 times. The first time was 3 weeks ago where I used a condom for the first half then took it off. The second time was 2 weeks ago where I was raw and she did something she thought was embarrassing and we stopped. She has undergone a lot of stress lately with her grandma dying, getting in a car wreck, school, and work so I think that's why she's late. I also have a condition called varicocele that's believed to make a man infertile although I know I can come. We are both very scared and do not know what to do.