Using the standard formula, your income is treated as being earned equally over the year. If you had a late lump sum and made a late payment, you can be considered underpaid for the earlier quarters.
The IRS calculates their own penalty and the Turbotax formula is rarely exactly right, if you pay a penalty now you still could get a few dollar refund or a few dollar extra bill. I would decline to allow Turbotax to calculate any penalty. Wait and see if the IRS bills you. If they do, you can request a waiver for cause or if it was your first time owing a penalty. You can't request a waiver if you pay the penalty on speculation.
