Form 5498-SA is form informational purposes and you do not need it to file your income tax return. See What do I do with Form 5498?

If you received Form 1099-SA Distributions from an HSA, Archer MSA, or Medicare Advantage MSA, make sure you entered that form in TurboTax. To enter Form 1099-SA, click on Where do I enter my 1099-SA?

If you received form 1099-SA and did not enter it, you may have to amend your income tax return. Wait for your return to be accepted or rejected by the IRS.

Wait for your return to be accepted or rejected by the IRS

• If the IRS rejects your E-Filed income tax return, you could change your return.
• If the IRS accepts your income tax return, use the amend feature in TurboTax. 
• Wait for the IRS to process your original income tax return before you amend it.  If you are expecting a refund, check for the status at  Where's My Refund? - It's Quick, Easy and Secure. - IRS.gov
• The IRS 2016 Amended tax forms/instructions will not be ready until some time in February. 
• See How to Amend (Change or Correct) a Return You Already Filed to amend your income tax return. Please keep checking the TurboTax FAQ for the status of amended return tax forms.

Your employer and your Health Savings Account contributions should by on your W-2, Box 12, Code W Code W—Employer contributions to a health savings account (HSA). If the information is missing, contact your employer.