Both are perfect. Either way you say it, the listener will mentally supply the missing words: "Yes, he is (my brother)." "Yes, it is (my brother)." Neither is better than the other. The difference is not in meaning. They say EXACTLY the same thing. The difference is your internal mental process as you speak. This is so often the case. For a similar example, consider these two sentences: "This is my brother." "That is my brother." They mean the same. The only difference is what is going on inside of your head. "This" is mentally close. "That" is mentally further away. Nobody can tell you which way you should say it because nobody can tell you what should be happening inside your head. So, what do you think when you point to your brother? Do you think about agreement between pronouns, or do you think that "he is my brother". Personally, I prefer "he is". It sounds more human to me.

Yes it is. It’s not wrong to say ‘yes he is’ but I’d use that reply more if the question was ‘is he your brother’ because the question could be taken to mean ‘is he your brother or your cousin or a friend etc’

I f you want practice english with me you can text me

He is