I suggest, take her out, preferably to an open place, like park or go for a long walk with her and bring the topic up in a tone that is not apprehensive. Tell her you know that she has a boyfriend and that you would have felt nice if she had told you rather than you finding out. Tell her that you trust her and you will be by her side in the choices she makes because you trust her and know that she will always live upto her values. You can go through this article, may be of some help. http://www.professorshouse.com/family/children/articles/daughters-first-boyfriend/
I have a 13-year-old son and I directly ask him if he has a girl in his life. I know its too early (for us) but at their age they think they are grown up. Don't beat around the bush and have a heart-to-heart "normal" chat with your daughter. Don't start preaching her instead give her the right picture about the consequences of the "wrongs"!
You need to speak to her and confirm your doubt. It is a very delicate situation and you don't want her to get taken aback and not speak to you on the issue. Re-assure her that this is a normal phase all teens go through and you are not annoyed with her at the same time you want her to know her what is acceptable and not. Guide her accordingly.
https://www.jw.org/en/publications/magazines/wp20131101/talk-to-your-teenager-without-arguing/
https://www.jw.org/en/bible-teachings/family/teenagers/ask/ready-to-date/
https://www.jw.org/en/bible-teachings/family/couples-parents/