I wonder if this is a bad school fit, making your daughter seem even more out of place than she might otherwise. Can you investigate other schools and find one that might have more grade skippers? In our state, we can see how many students are identified as gifted at each school, which is a good way to gauge if there might be more kids like your daughter. Also, it seems like your daughter might fit in well at a STEM-focused school, where they might even have Minecraft clubs (my son's school does!).
We went through this with my son. Third through 8th grades were the hardest. The fact is, he just didn't have that much in common with age peers. They weren't that interested in him, and he really didn't have an interest in trying to fit in with them. He thought they were all immature and not very smart. After homeschooling a while, we finally found the right school for him. There was a period of transition when he started, but this year he is having such a fantastic year, I can't even believe it. He says repeatedly how happy he is, which is surprising to hear from a reserved, sarcastic kid.
In the meantime, I would reassure your daughter that things will get better, that you are working on it, and you'll help her find a solution. Tell her it's not HER, it's that the other kids just aren't at her level yet. I would also look for clubs or activities outside of school that she might be interested in, like a minecraft club (can you start one?), or an art group.
