How to report removal of excess Roth IRA contribution?

If you know what the gains are, you can enter them now instead of amending later.  Create a substitute 1099-R with the total amount of the withdrawal in box 1, the taxable amount (attributable income) in box 2a, and use codes P and J in box 7.

Typically, most people would enter the Roth contribution, then be told by Turbotax that it is not eligible, and be recommended to remove it.  However, the result of doing that is that nothing is reported on the tax return, so you don't have to follow those steps if you don't want to.  Just leave the Roth off the return, and report the 1099-R now or later.  (Roth contributions are not reported unless they are un-removed excess.  There is nothing reported on the tax return that you made a Roth contribution if you later removed it within the deadline.)

The 5498 doesn't change because that's what happened in 2024.  If the IRS actually tries to reconcile the records (and there is some evidence that they don't bother even though they make it seem like they do) then the 5498 will be offset by the 1099-R with codes P and J. 

@RogerD1  @AnnetteB6  My situation matches that of the original post, except for one thing — the excess was removed late — approximately 13 days AFTER the extended October 15, 2025 deadline.

I contributed $8,000 towards my 2024 Roth IRA prior to the April 15, 2025 tax filing deadline expecting my total income would fall within the eligibility limits for Roth IRA contributions. Due to filling for the extension, then discovering very late it was an excess contribution of $8,000 to my Roth IRA, and then processing delays with my Roth IRA custodian, I filed my 1040 on Oct. 15, 2025, with form 5329 correctly reflecting the $8,000 excess contribution at the time of filing. Because of this, I was assessed the 6% penalty ($480). However, as stated above, I fully corrected this with my IRA custodian with a complete removal of the excess contribution, but again, after the deadline.

My questions is - How do I handle this so that that penalty is excused? Since my Roth IRA excess contribution was removed eventually a few days after the allowed period, should I file an amendment (1040-X) now reporting $0 on 5329? And then also request a waiver of that $480 penalty with a letter of explanation?

Thanks.