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Hmmm" may refer to different meanings in different contexts, usually depending on the person using it.

Most common usages being :-

The person is still pondering over your message and will come back with an apt reply soon.

The person totally agrees with your message and it's a kind of "yes".

The person doesn't agree with you and is still thinking over it and may soon reply why he doesn't agree. Usually a " Hmmm" followed by a "but".

The person got bored by the conversation and is showing lack of interest. This is when you get a lot of " Hmmm"s as replies for most of your messages.