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If you need to file an amended tax return after IRS accepted your tax return due to a mistake or a missing document, then you will need to wait until your original tax return is processed by the IRS. All documents are filed with the IRS, so you will want to make sure that all documents are entered on your tax return. If you are receiving a refund, you should wait until the check is issued. Amended returns must be filed by mail.
The article below has the specific 2016 instructions to amend a return.
https://ttlc.intuit.com/replies/3288565
When you mail Form 1040-X you should include the following forms:
Please note that 1040-X cannot be e-filed - you will need to mail a paper return. It takes the IRS at least 2 - 3 months (and sometime up to 6 months) to process amended returns. Also, depending on whether the changes affect your numbers, you may also be required to file an amended return with your state.
The mailing address for you state and situation can be found at https://www.irs.gov/pub/irs-pdf/i1040x.pdf. Look under Where to File on page 14.
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