Which of the following words describes the subtle differences in meaning that synonyms can possess?

context

nuance

prefix

definition

The word that describes the subtle differences in meaning that synonyms can possess is nuance.

That is the very definition of that word - "subtle difference in meaning." It doesn't only refer to synonyms, but to anything in general. But when it comes to synonyms, regardless of the fact that those are words that have the same meaning, there are still many cases where you would use one synonym, but not the other, because their meanings are not completely the same.