I can’t think of any other ‘it’ that is meaningless. ‘It’ normally refers to something in the sentences context. But in that and in the sentence ‘it rains’ there is nothing that ‘it’ could refer to. The sky doesn’t snow, the weather doesn’t snow and neither do the clouds.
The sentence does make sense, because all the speakers understand what it means. The context is implied, as another commenter linked to.
Which sentence do you mean?
the one you were talking about not making sense: “it is the case”
you’re both kinda agreeing on the same thing, whatever the “it” is, is understood through context. which when you lack said context, the sentence becomes nonsensical