If you've been using TurboTax all this time and have been doing SEPP withdrawals for several years, but you don't remember being asked about whether they were SEPP withdrawals before, you may want to look at your previous tax returns to make sure that the early withdrawal tax was not paid. This would show up on Part I of Form 5329. You may find it worthwhile to amend your previous tax returns if this tax was added in the past.
Wow. I checked my 2017 return. Part I of Form 5329 is blank. I'm guessing that the "Distributions not subject to additional tax smart worksheet" should list the distribution amount next to "Equal periodic payments"?
What are non-simple versus simple distributions?
I noticed that in TurboTax it says "Based on your entry [code 2 D] for box 7 on your 1099-R, you don't need to pay any extra taxes on the money taken out of this account."
Maybe the 10% that was withheld by Vanguard was for the pre-age 59 1/2 10% penalty, and not for like an estimated tax prepayment.
If I overpaid on taxes then I'm guessing that the IRS only lets me look back 3 years for refunds.
On my 1099 why wouldn't the IRA/SEP/SIMPLE box be checked?
If your 2017 Form 5329 Part I is blank, that means that you were not charged the 10% early withdrawal penalty. If that is true, then you would not need to amend 2017 in order to get the 10% penalty back, because you didn't pay it. (If you had paid it, you would see it on line 4 of Form 5329.)
What is the context for "simple" vs "non-simple" distributions? I haven't seen that in any IRS stuff I've read. Is the word SIMPLE capitalized? If so, that's a kind of retirement account I believe, and wouldn't apply to you as you apparently don't have a SIMPLE account.
As implied, it would be good to check your 2018 Vanguard 1099-R and your return as well to see what happened there.
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I dug into it a little more, and the fact that Vanguard is putting a code 2 in box 7 (in addition to the code D) means that they know that it is part of an SEPP. Because they know that and because they put a code in box 7, that means you're not subject to the 10% penalty. The tax program knows that because of the code, and doesn't fill out Form 5329 (at least, not Part I, which is the relevant part for this part of your tax situation.)
It is likely that Vanguard has reported your distributions in 2017 and 2018 with code 2 as well.
I'm not sure why Vanguard withholds 10%. It would likely be estimated taxes if the distribution is considered taxable income.
The reason the IRA/SEP/SIMPLE box is not checked is because what you have is none of those things.
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https://www.irs.gov/pub/irs-pdf/i1099r.pdf)