Is it normal for a twelve year old boy to have one testicle larger and lower than the other?

Anatomy: Yes. Of course. One testicle is always more dominant than another.

Here are some ...: The level and size of both halves of the scrotum is not same and symmetrical with no prevalence to either side among most of males, at least to a degree. As to the size of testicles, that usually needs to be professionally palpated, estimated or measured with experienced hands or a ruler' but largely, the size & consistency of both testes are quite symmetrical. So, use these to discern & confirm..

Probably normal: One testicle sitting lower is normal, as is one testicle being a little larger. As long as this isn't an acute change, or associated with pain, it probably is HIS normal. Have your doctor evaluate this at his next physical