Well, the first thing to understand is that there no 'extra' skin - whatever you're seeing in your vagina is probably meant to be there.
The vagina isn't just a smooth, featureless tube-shaped hole. There is a lot of flesh (inside and out), as well as having a cervix and g-spot.
It's hard for me to answer your question because I'm not sure where this skin is located. It could be part of your hymen (also called a 'cherry'), your cervix, or just a bit of flesh you've not noticed before.
Chances are everything is fine. I can understand your being worried to discuss this with your mother, but if you choose to discuss it with anyone you can just say you are observing your body - after all, it's in the interest of your health to do so.
If you're 16 you're about the age that you'll be needing to see a gyno for the first time (even without having sex). That doctor will be able to examine you and put your mind to rest about anything you're unsure about.
Best of luck.