John Gill Commentary 1 Samuel 3:4

"that Jehovah called Samuel; and he said, Here am I." — 1 Samuel 3:4 (ASV)

That the Lord called Samuel
By a voice which came forth from the most holy place, from between the cherubim, the seat of the divine Majesty:

and he answered, here am I ;
which was not intended to declare the place where he was, but to express his readiness and cheerfulness to do any thing that was required of him.