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I will need to file an amended return this year. I will owe $36 in federal taxes. My original return had zero tax owed (and zero returned). I would like to make a payment for $36 to prevent any issues later on.

According to the IRS website:

Taxpayers filing an amended return because they owe more tax should file Form 1040-X and pay the tax as soon as possible. This will limit interest and penalty charges.

When I go to the IRS website to make a payment, it asks for the reason for payment with a dropdown box, but I'm unsure which option is the correct one. The relevant options seem to be

Tax Return or Notice

Make a payment on your recently filed original (not amended) return or for a balance due on a notice. Please note: As a reminder, your payment satisfies your payment obligation only. Filing your return is a separate process that must be completed. IRS Direct Pay only accepts individual tax payments.

Extension

Make a full or partial payment on your taxes in order to receive an extension without filing Form 4868, Application for Automatic Extension of Time to File for U.S. Form 1040 Individual Income Tax Return. Reminder this is an extension of time to file and not an extension of time to pay.

Estimated Taxes

Make estimated tax payments in advance of the timely filing of your return. Depending on your income, your payment may be due quarterly, or as calculated on Form 1040-ES, Estimated Tax for Individuals. You do not have to indicate the month or quarter associated with each payment.

Proposed Tax Assessment

Make a full or initial payment for a proposed amount due based on a CP 2000, a Notice of Deficiency, or other proposed assessment to your return. Payments of this type may post in advance of the actual tax assessment. If you have an installment agreement, select Installment Agreement as the reason for payment.

Amended Return

Make a full or initial payment on a recently filed Form 1040X, Amended U.S. Individual Income Tax Return, or when an amendment to your return results in a balance due to your Health Care Individual Responsibility (also known as Shared Responsibility). If you are making additional payments for a previously filed 1040X, select "Installment Agreement" or "Tax Return or Notice" for 1040 payments or Health Care Individual Responsibility payments.

The first option, "Tax Return of Notice", apparently doesn't apply, since my original tax return showed that owe $0.

The second option, "Extension", does not seem to be the right fit. I have already filed and will be amending, I am not requesting an extension

The third option appears to be the right one, I want to pay estimated taxes owed. However, when I pick it, the second dropdown box "Apply Payment To" is automatically set to "1040ES (for 1040, 1040A, 1040EZ)" (which is fine, I am filing a 1040), and the third dropdown box "Tax Period For Payment" is set to 2020. But I am trying to pay taxes for 2019!? It does not let me change this to any other year.

The fourth option "Proposed Tax Assessment" seems like it is probably the correct one, even though I have not received a "CP 2000, a Notice of Deficiency, or other proposed assessment to your return."

The last option "Amended Return" I assume is not correct either, because I have not filed the 1040X yet.

I hope someone can help clarify which of these options is appropriate (or if the choice will actually matter in terms of avoiding penalties for unpaid taxes)

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I wouldn't bother. If you are going to file the 1040-X reasonably soon -- within a month, or two at most -- just pay the tax then, either by including a check or making the electronic payment. Since the interest you at least nominally owe is computed starting from the filing deadline, which was delayed due to COVID, it will only be about 10 or 20 cents. I guarantee IRS won't even try to collect that -- when they do RoI calculations they have to include a lot of overhead and downstream items that make it 'cost' something like $10, so from their point of view merely mailing you one notice is a 'loss'.

But if you really want to, use 'Amended Return'. They don't know you haven't mailed it yet, and with the current operational disruptions probably won't even try to match for at least 2-3 months. As long as the return is in the system by then, even if not fully processed, the credit amount will be 'locked' until posting completes.

You are aware, I hope, 1040-X still has to be mailed on paper? ETAAC finally this year got management to agree to add 1040-X to e-file (MeF) after like a decade of trying, but it will still take several years to get implemented and deployed -- not soon enough for you :-(

'Estimated tax payment' is a term of art here. It doesn't just mean a payment that you estimated. It means payments made during the tax year, and by specified dates -- called 'quarters', although they aren't quite. That's why the website currently will only allow 'estimated' payments for 2020, and it will automatically choose the current 'quarter' which you can't change either. Note 1040-ES is actually a separate (and very simple) form, NOT a variant of 1040 (or 1040-X), although the paper form is used only for physical payments (check or cash); electronic payments are simply flagged as 'for 1040-ES, SSN XXX [and YYY] as of date DD'. (If you want, you can download 1040-ES from the website in PDF and look at it. In normal times you can also phone the publications number and have them mail you a paper copy, but right now I don't think that's working.)

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