If you want to file an amended tax return after IRS accepted your tax return due to a missing W-2, then you will want to wait until your original tax return is processed by the IRS. If you are receiving a refund, you should wait until the check is issued. Amended returns must be filed by mail.
To amend a 2016 return, follow the steps in the article below: https://ttlc.intuit.com/replies/5114064