I received a tax penalty, seemingly because I owed too much tax. If I amend my return, and the amendment decreases the owed amount, can I get back the penalty?

[vcntlee-umich-ed]

To add to my question, I have already paid the amount owed in my federal return to the IRS, this amount includes said penalty (Line 38 of Form 1040: "Estimated tax penalty"). However, a few weeks later, I noticed a 1099-B capital loss that I forgot to include in my tax return, so I filed an amendment. This would decrease the original amount I owed to the IRS by roughly $1000. Seeing that the owed amount is less, will I be able to see some of that penalty refunded back to me?

[VolvoGirl]

So you should be getting a refund with the amended return.  Don't figure in any penalty.  The IRS might refigure it for you or pay you interest with your new refund.

The amended return will only be the difference you get back or need to pay. You can confirm this by printing your amendment and looking at the 1040X. Line 18 should be your original refund amount and line 21 should be your additional refund.  If you paid on your original return it will be on line 16 (but don't include any penalty on 1040 line 38). If there is an amount owed with the amendment, it will be on line 20.

IRS Instructions for line 16……
You are filing Form 1040-X to amend your tax return. You sent a check for $1,500 with your original return, reflecting a payment of $1,400 in taxes and a $100 estimated tax penalty. When completing Form 1040-X, enter $1,400 on line 16 (the check sent with the original return minus the $100 penalty).