I think I got this as a Kindle book, might have had more than one book in the series (and I'm pretty sure it was a series). The girl's mother never let her leave the house, and is constantly training her in martial arts and survival skills. I think when her mother is out of the house, she's required to stay inside a refrigerator-size box in the basement for her own protection. One night, while her mother is out, her house is broken into by two men with supernatural powers (extremely strong and tough, I think) and in the process of escaping them, she escapes the house. Not long after that, she gets hooked up with some secret society out to protect humanity with other people with powers trying to hurt people (or maybe just grab power). The girl, of course, has her own sets of powers. I want to say that it's revealed that all of these powers come from mythological ancestry, with the girl being descended from the Greek line. I also want to say there was someone with Gorgon or Medusa ancestry, although I don't remember if they were good guys or bad guys.
I don't have a firm idea on when I read this. I think it was part of a bunch of books I got for free from a site like Plenty Of Ink, basically promotional copies in hopes that you buy later entries in the series. That would like put them about 7 years ago. I don't think it was less than five years ago, because I'm remembering it as an early acquisition.