Talk to the guidance counselor.
Your daughter may be feeling more sensitive about not fitting in than necessary. I mean, has she actually tried sitting with her acquaintences or does she just assume that they will ignore her? It's hard putting yourself out there sometimes, especially when you're a freshman.
Both of my kids were always enlisted (and happily complied) with taking the new or shy kids under their wing. They showed them around, ate lunch with them, introduced them to other kids. My kids were often buddied up with special needs children as well because they treated them just like any other kid.
My son was a freshman last year, and even though he had all of his friends from elementary and middle school there at the same time, one of the most popular jocks in the entire school assigned himself to my son. He not only showed my son around, but showed my son where HIS locker and classes were, ate lunch with him and told him that if anybody messed with him or treated him badly to let him know and he would deal with it. My son thought it was AWESOME! The truth is....it's nothing different than my son had always done for other kids and now that he's a sophomore, he looks out for the freshman.
Your daughter is NOT a loser, she's not a charity case or anything, but I'll bet you there are kids that are known for having a knack for inviting other kids in. I'm sure her school knows exactly who they are.
High school is hard. Adjusting to everything the first year is tough. It's all new, but she will find her way and settle in.
The other thing is, none of the clubs hold appeal to her. There are no clubs for her particular interests. How does she know if she doesn't try? If she doesn't at least go to a meeting to see if it's what she might like or not?
It's hard putting yourself out there, but she can't wait for engraved invitations and a red carpet rolled out....
Being picky and isolating herself won't help anything.
Maybe someone can buddy up with her until she gets the confidence to reach out. There are so many opportunities to really have fun in high school.
I think she'll get it figured out.
Best wishes.