When an underpayment penalty is calculated on a tax return, this penalty is automatically added to the amount you owe on Form 1040, Line 78 (or Form 1040A, Line 50). If you are entering information on IRS Form 1040X, Line 16 Tax Paid With Original Return, you will want to keep in mind that the underpayment penalty may have already been included with the amount you originally owed/paid.

You will want to make sure you subtract Form 1040, Line 79 from Line 78 (or Form 1040A, Line 51 from Line 50) before entering the amount on the Form 1040X.