When an underpayment penalty is calculated on a tax return, this penalty is automatically added to the amount you owe on Form 1040, Line 23. If you are entering information on IRS Form 1040X, Line 16 Tax Paid With Original Return, keep in mind that the underpayment penalty may have already been included with the amount you originally owed/paid.

Make sure to subtract Form 1040, Line 24 from Line 23 before entering the amount on Form 1040X.