Unfortunately, once your return has been submitted for e-file, you cannot make any changes to add the 1099-SA until it is either Accepted or Rejected. The IRS will not receive the change.
Then, when/if the Return is accepted, you will file a new amended return. If your return is Rejected, you can go ahead and make the change and then resubmit the e-file.
Amending is done on Form 1040X. That form should be available for amending 2015 returns mid-February. Also, if your return is accepted, you should not try to amend your return until it has been fully processed and you have received your refund or your payment has cleared.
Amended returns have to be printed and filed by mail. It can take the IRS up to 12 weeks or longer to process them. If you are due a larger refund than on your original return, your amended return should only show the difference and you will receive a separate check for it. If you owe money on your amended return, it will show only the new amount owed, you will have to mail a check with the return.
How to Amend?
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