If you have an underpayment of estimated taxes penalty it will be entered on your federal tax return, Form 1040 Line 38. The amount on Line 38 is included in the taxes owed or it reduced the amount of tax refund.
IRS Tax Topic for the underpayment of estimated tax penalty - https://www.irs.gov/taxtopics/tc306
If you get a penalty on 1040 line 38, you might be able to eliminate it or at least reduce it. You can go to Federal Taxes tab or Personal tab, under Other Tax Situations and select Start by the Underpayment Penalties. You will answer a series of questions that may reduce or eliminate the penalty. Or you can elect to have the IRS figure the penalty for you. It's form 2210.
How to add form 2210 for Underpayment Penalty
https://ttlc.intuit.com/community/tax-payments/help/how-do-i-add-form-2210/00/25703
It's under
Federal or Personal (for Home & Business Desktop)
Other Tax Situations
Additional Tax Payments
Underpayment Penalties - Click the Start or update button