Yes, there would be penalties in the case you outline. But the amount is based on the tax return you file.
If you owe more than $1,000 when you file your taxes, you could be subject to a penalty.
The IRS calculates this penalty by figuring out how much you should have paid each quarter and multiplying the difference between what you paid and what you should have paid by the effective interest rate for that period. This means you can have a penalty for one quarter, but not the others.
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