ペンです。It is a pen.
Really, this is missing a hidden subject, so it’s really “[It] is a pen”.
[それは] ペンです。[それが] ペンです。[It/That] is a pen. それ is a hidden subject.
(Notice I’m calling it “subject”, which as you know could be marked with subject が or topic は, depending on the situation.)
You can replace です with an equal sign.
it = pen
For context, this is the answer to a question like this:
このへんなものは、何ですか!What is this weird thing!
それはペンです。That is a pen.
ペンがある。Literally, A pen exists. => There is a pen
Here, you’re talking about the existence of a pen, not that it’s equal to something.
The pen is the subject. You’re describing that the pen exists in the world, not describing some characteristic of it.
For context, this is the answer to a question like this:
ない!ない!いいアイデアを書きたいんですが… There’s nothing! There’s nothing! I want to write a great idea, but…
ほら!あそこに!ペンがある!Hey! Over there! There’s a pen!