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The IRS has not yet started accepting e-filed tax returns. They are scheduled to begin on February 12. There is still a chance your return will be rejected. If it is, you can add your 1099-SA. If your return is accepted, you can do one of two things: 1) File an amended return, or 2) Wait for the IRS to send you a letter proposing an adjustment to add $686 to your income. You can respond to their letter and explain that you received Form 1099-SA after you transmitted your return, so you didn't (correctly) file Form 8889.
I would wait to see if your return is accepted, and if it is then wait until you have received any return you are expecting, and then file an amended return. To file an amended return TurboTax, see:
Can I just adjust my taxes before they are processed?
I see them as “pending” status.
i am concerned that by the time I re-file I will be charged for using TurboTax service because the promo window is gone. Can you ensure this will not happen?
No, unfortunately you cannot change your taxes before they are accepted. DavidD66 gave the correct advice about waiting to see if you return is accepted.
Form 8889 which is used for a Distribution from an HSA is not included in the free file tax return. This must be filed with the Deluxe return. See the forms in this link: Forms Included with TurboTax Products.
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