I would not file an amended return at this time as the IRS is still processing your original return. Filing an amended return now will delay your processing by a lot as the IRS will have to process 2 returns at the same time in different departments. When the IRS is finished processing your original return, you are more than likely going to get the CP2000 notice, which is for missing income.
I recommend you create an account with the IRS. Then go and get online your wages and income transcript for the year 2024. Keep your original return handy along with the 1099-MISC and the wage and income transcript.
Once you hear from them, if you may consider amending your return to see if you agree with the IRS outcome of income and taxes.
Once you receive the CP 2000 notice, you can agree and pay or disagree and not pay or partially agree with them. You will have a chance to respond to the notice they send you.
As to your question about the penalty assessed by Turbo Tax, once your return is processed and you amend your return, you can go to the penalty section and then use the annualized income screen to say that this withdrawal was made in the 4th quarter. Then the penalty will not be assessed on it as the estimated taxes will have been made timely. You should include Form 2210 with your return.
