Possibly. If you owe tax when you amend, and it is after April 15, you may owe 0.5% penalty and 0.5% interest per month on the amount you owe. For a $5000 IRA, you probably will owe $1250 in extra tax, so $26 penalty plus interest if you amend and pay before May 15, $52 if you amend after May 15 but before June 15, and so on.
You can also request a penalty waiver if this is your first time with a penalty, but the interest can't be waived by law. Don't pay a penalty with your taxes when you amend even if Turbotax offers. Wait to get billed.
Abatement https://www.irs.gov/businesses/small-businesses-self-employed/penalty-relief-due-to-first-time-penal...