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To avoid penalty, you need to have paid thru withholding or timely estimated tax, the smaller of 100% of your 2023 tax (110% if AGI > 150k) or 90% of your 2024 tax.  You can also do this safe harbor calculation manually to verify the TT calculation and then need to understand why IRS calculated differently.   TT calculates penalty based on the information it's been given for 2023 AGI/tax and estimated tax payments.  IRS calculates it independently based on information in their systems.  If they came back with a different result then you should check if there was any adjustment to your 2023 or 2024 AGI/tax that wasn't reflected in TT, or if you paid estimated taxes check that the IRS has the same amounts and payment dates as TT by checking your account on irs.gov.   If you are using TT desktop in Forms mode you can double click on line 38 on Form 1040 and again on the worksheet to bring up the Form 2210 calculations.

Did you complete an IRS Form W-4 for your federal withholdings and give it to your employer? - https://www.irs.gov/pub/irs-pdf/fw4.pdf   Go to this IRS website for a withholdings estimator - https://www.irs.gov/individuals/tax-withholding-estimator

@vmuralid  You can get Form 2210 and 1040-X in fillable PDF fromat from IRS. If you fill out Part 1 correctly you will confirm either TurboTax (zero) or IRS (not zero).     If you want to request a waiver of IRS's amount using 2210 Part II Box A, or point out your result of no penalty, or both, attach Form 2210 to Form 1040-X and mail it in.   Penalties: 1040-x Line 16: Subtract any penalty from the amount you owe reported on original 1040. (in your case Zero) Don't try to include, but ignore, any new or changed penalty. IRS will calculate your new penalty on their own and will bill you. Note: when you are not changing any dollar amounts on your amending 1040-X, you can leave all the lines 1-23 EMPTY.   Don't even think about including your old 1040 nor your revised 1040 because the Form 1040-X reflects any changes there and becomes your new tax return.

Review this IRS website for the penalty and how to remove or reduce the penalty - https://www.irs.gov/payments/underpayment-of-estimated-tax-by-individuals-penalty   If you are using the TurboTax desktop editions, then you can access the Form 2210 using Forms mode.  Click on Forms.  When in Forms mode click on Open Form at the top left of the screen.  Type in 2210 and then click on the result to open the form.   If you are using the TurboTax online editions, then you will have to complete the Form 2210 using the IRS website. Go to this IRS website for the Form 2210 - https://www.irs.gov/pub/irs-pdf/f2210.pdf Go to this IRS website for the Form 2210 Instructions - https://www.irs.gov/pub/irs-pdf/i2210.pdf

No one in the user forum can resolve a billing issue.  If you have a question about your TurboTax fees or billing, make sure you use the word “billing” in your request for help.  Do not use the word “refund.”   https://ttlc.intuit.com/turbotax-support/en-us/help-article/account-management/contact-turbotax/L2y9ZKpQB_US_en_US?uid=m5s9l2vh

Line 38 of 1040SR shows as blank.  However, as explained in original question, IRS has sent a letter charging me a penalty for failing to pay estimated taxes.   As indicated, this means there is an error in TurboTax calculation (which they guarantee against) or the IRS calculation (based on return submitted through TurboTax).   Please advise on how to respond to IRS.

Did you mail your tax return and your son's tax return in the same envelope?  If so, then the IRS probably just processed his return and your return has been discarded.   If this is the case then mail your tax return again and this time use the certified or registered mail from the US Post Office.

I want to prepare a state return.    When you use TurboTax the information flows from the federal return to the state return.  You cannot use TT to prepare a "stand alone" state return.  Try going to your state's tax website to see if you can file there.   CONTACT THE STATE   https://ttlc.intuit.com/turbotax-support/en-us/help-article/state-taxes/contact-state-department-revenue/L9qVToi02_US_en_US?uid=m6e06um0

That paragraph only addresses a contribution returned before the due date of the tax return, the contribution made for 2024 in this case.  Excess contribution distributed after the due date of the tax return for the year for which the contribution was made is not corrected until the year of the distribution, in this case 2025 for the 2021, 2022 and 2023 excess contributions.