I made an IRA deposit on April 15th, but the transfer was cancelled by the bank. Will I end up with a penalty once I amend my return?

I opened an IRA account on April 15th attempting to transfer funds from my bank account.  I mistakenly used an account the bank had closed, and so the transfer was rejected.  I now need to file an amendment to remove the $3000 IRA contribution.  Will there be a penalty?  Any other ramifications?