First, you have to make sure that your return was accepted by the IRS. If it was, then you should wait about three weeks (or until you get your refund), to ensure that the IRS has finished its processing of your return.
Then you will need to amend your return, adding the 1099-MISC. To amend your return, see this.
If you do this before April 15th, then there should be no penalty. It really depends on whether or not you are going to have a tax due because of the 1099-MISC. If your withholding will cover your 1099-MISC as well, don't worry about a penalty.
You can always file an extension, paying what you believe will be your tax including the 1099-MISC. To file an extension, please see this link.
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