What does it makes sense mean?

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Ok I'll be really specific- sense can have different meanings- you have to infer with context clues to figure out which is being described.

1. any of the faculties, as sight, hearing, smell, taste, or touch, by which humans and animals perceive stimuli originating from outside or inside the body. example: My sense of smell is really strong.

2. a feeling or perception produced through the organs of touch, taste, etc., or resulting from a particular condition of some part of the body. Example: to have a sense of cold.

3. to perceive (something) by the senses; become aware of.
Example: I sense someone is following me.

4. to grasp the meaning of; understand. Example: I can now get a sense of what you mean. It's easier when you explain it with visuals.

A little trickier... Idioms
1. come to one's senses, to regain one's good judgment or realistic point of view; become reasonable. Example: I'm telling you that's a bad idea... If you don't come to your senses now, I'll slap you.

2. in a sense, according to one explanation or view; to a certain extent. Example: In a sense it may have been the only possible solution.

*With what I gathered from your question- I think the 4. is the one you are asking in regards to.