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If you did not make any contributions to your HSA or your MSA other than through your paycheck, then you don't need to worry about your 5498-SA. This form is sent to you for information only. You will need to enter the amount on your W-2 in Box 12 with code W. You will not need to enter anything further about contributions to your HSA.
You will only get a form 1099-SA if you withdrew money from your HSA. These forms must be furnished to the recipient by January 31, so you should have gotten yours by now.
When you put money into a retirement account through work, you do not need to report it (assuming you meant 401k or similar). If you contribute to a retirement account outside of work, you need to report that, since there are restrictions on how much you can contribute.
Here are links to the various types of retirement plans.
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