After the IRS send whatever refund they decide is proper......if the amount they send still indicates they retained the penalty? Then:
Sometime in (say) May, you could prepare an Amended tax return to see if you can get the penalty partially-or-all refunded......BUT...that is not worth the effort if your penalty was less than ~$50 or so....because it's a lot of work on your part.
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Do Not start an Amended tax return now...wait until you see what the IRS does...
To amend to see if you could change it (Wait until May), you'd start an Amended Federal tax return. Then you'd go to the "Other Tax Situations " page and start in on the Underpayment Penalty section. In there you will need to delineate all Your income, wages, 1099-R, SS, dividends, Interest, Cap gains, deductions, credits for estimated payments, withholding etc...all delineated by quarter...and the "quarters" are uneven and are 3mos, 2mos 3mos, 4mos. That will fill out an "Annualized Income" form 2210AI, and the associated 1040X for you to e-file.
(might need to Amend state too....but if you didn't have a penalty there, it probably wouldn't be needed)
So you need all your monthly statements and perhaps a spreadsheet. TTX tries to lead you thru it, but it's still a bit complicated. You can go thru it several times as you see what details you need to provide and modify your responses appropriately.
But like I said, if the penalty was small, don't bother...and don't be tempted to touch your tax file for a couple months anyhow.
____________*Answers are correct to the best of my knowledge when posted, but should not be considered to be legal or official tax advice.*
