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Something similar happened to me last year with a CP2000. What worked for me was writing a letter requesting "interest abatement" under IRC 6404(e). That's the specific tax code that allows the IRS to reduce interest in cases where there was unreasonable delay caused by an IRS officer or employee. I specifically pointed out the dates: when my original return was filed, when the income information would have been available to the IRS from third parties, and the date they finally sent the notice. I made the case that the delay was excessive and beyond normal processing time. They actually approved it and removed about 8 months of interest charges! Make sure to be super specific about the timeline in your letter and cite the specific law. It needs to go to the specific department listed on your CP2000, not just general IRS addresses.
This is super helpful, thank you! How long did it take them to respond to your abatement request? And did you have to provide any specific evidence beyond just pointing out the timeline?
It took about 6 weeks to get a response, which was actually faster than I expected. I didn't need special evidence beyond clearly outlining the timeline with specific dates. One tip - I made sure to include all the reference numbers from the CP2000 notice at the top of my letter and made it very clear I wasn't disputing the actual adjustment, just the interest. I think that helped it get processed faster since they knew I wasn't challenging the underlying tax assessment. I also kept it to one page and very factual - no emotional language about how unfair it was. Just dates, facts, and the specific tax code.
Has anyone tried calling the Taxpayer Advocate Service about this kind of issue? I had a similar problem with a different notice and they were actually pretty helpful. They're technically separate from the IRS and can sometimes intervene when there are hardships or unfair procedures.
I tried the Taxpayer Advocate last year for a similar issue but they told me they couldn't help because it wasn't an "economic hardship" situation. Seems like they're really only equipped to help if you're facing immediate financial difficulty, not just regular interest disputes. Worth a shot I guess but they're also super backed up these days.
Good point about the hardship requirement. I think my situation qualified because I was facing a lien at the time. For regular interest issues, probably better to go with the interest abatement request directly to the IRS like others mentioned. The Taxpayer Advocate is really more for when you're truly stuck in the system or facing serious consequences.
I work at a tax office (not an accountant, just admin) and see this issue frequently. The IRS has been particularly bad with SEP IRA deductions lately. Look carefully at your 5498 form from your financial institution - make sure the contribution is properly marked for the correct tax year. We've had several clients where the financial institution reported the contribution correctly but checked the wrong tax year box. When this happens, the IRS computer automatically disallows the deduction because they can't match it to their records.
That's really helpful! I'll double check my 5498 form. Is there a specific place on the form where it shows which tax year the contribution is for? My contribution was made in April 2025 but designated for 2024 tax year.
Look at Box 8 of Form 5498. It should specifically indicate "SEP contributions" and show the amount. Most importantly, the form should have the correct tax year printed at the top (2024 in your case, even though it was issued in 2025). If the form shows the contribution but lists it for the wrong year, ask your financial institution to issue a corrected 5498. This happens more often than you'd think, and most institutions can fix it pretty quickly if you point out the error.
Just wondering - did you check if the IRS applied the refund to any past tax debts or other federal debts? Sometimes they'll take part of your refund for things like old student loans or past tax bills without very clear notification.
Good thought! I checked the transcript pretty carefully and didn't see any offsets or redirects of the funds. It specifically shows they just calculated a lower refund amount because they zeroed out the SEP IRA deduction line. No other debts or issues mentioned.
That's definitely an IRS processing error then. One more tip - when you do call them, make sure to use the specific phrase "math error authority" when explaining your situation. This is a technical term they use internally and can sometimes help get your case to the right department faster.
One important thing to note that hasn't been mentioned yet - the timing of your return of excess contribution matters a lot. If you withdraw excess contributions before your tax filing deadline (including extensions), you won't be taxed on the earnings from those contributions. But if you miss that deadline, you'll have to pay a 6% tax on the excess amount for each year it remains in your account. So even though your distribution wasn't coded properly, the fact that you took it within the same tax year is good!
Does the timing issue apply differently for Roth vs Traditional IRAs? I have a similar situation with both types of accounts and I'm confused about which deadlines apply to each.
The timing rules are actually the same for both Roth and Traditional IRAs. For both types, you need to withdraw excess contributions (and any earnings on those contributions) by your tax filing deadline including extensions (typically October 15th) to avoid the 6% excise tax penalty. The main difference is in how the earnings are treated. For Traditional IRAs, the earnings are generally taxable in the year you make the withdrawal. For Roth IRAs, the earnings are also taxable if you withdraw them, but they may additionally be subject to the 10% early withdrawal penalty if you're under 59½ and don't qualify for an exception.
Has anyone used Form 5329 for this type of situation? I'm wondering if I need to file that along with my tax return when dealing with the improperly coded distribution.
Quick question for anyone who's done this: if the entire $6000 was excess, does Vanguard just close your Roth IRA completely? Or do they just remove the money but keep the account open?
Word of warning from someone who procrastinated on fixing an excess contribution - the 6% penalty really adds up over multiple years. Don't wait to fix this! I ended up paying almost $1100 in penalties because I waited over 3 years to correct mine.
Jasmine Hernandez
My stepdad was in a similar situation and he just decided to liquidate everything without checking the basis issues first. Ended up owing way more in taxes than expected because there was no step-up and he had to use the original basis from like 40 years ago. Don't make that mistake! Get a proper analysis before you sell anything. Either use one of the services mentioned above or talk to a CPA who specializes in trust taxation. The rules around irrevocable grantor trusts are really specific and depend on how the trust was structured.
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Luis Johnson
ā¢Can confirm this happens a lot! I'm an estate paralegal and see people make this mistake all the time. The basis rules for irrevocable trusts are completely different than for assets inherited directly. One detail can make all the difference.
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Ellie Kim
Another option to consider if the stocks have declined in value and you're concerned about taxes - you could distribute the stocks to the trust beneficiaries first, then they could sell them individually. Depending on the beneficiaries' tax situations, this might provide better overall tax treatment, especially if any of them are in lower tax brackets. But this would depend entirely on the terms of the trust and whether distributions of stock (rather than cash) are permitted. Worth discussing with your trust attorney if that's an option.
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