SEPT IRA Excess Contribution and Amending Return

Hello,

 

For 2018 taxes, Turbo tax calculated my maximal SEP IRA contribution as $549.00. I filed my 1040 with a contribution amount of $549.00 to SEP IRA.  However, I made a mistake and requested Vanguard to contribute $686.00 towards my 2018 SEP IRA account.  Now I have a discrepancy of  $137 between what was filed and what was actually contributed to Vanguard.  Vanguard can remove the excess contribution plus the interest before Oct of 2019 deadline, but they said that I need to file an amendment and they will issue a 1099-R.  I have an concern with amending my taxes because if I amend taxes for 2018 with the same SEP IRA contribution of $549.00 (correct maximal contribution) then it might be look as no changes were made to the return.  Should I amend the 2018 tax to reflect a lesser contribution amount than $549.00 and have Vanguard remove the excess to match? Also, the 1099-R issue from Vanguard would mean that I would to pay taxes on the excess of $137 when I never received any deduction due to reported a contribution of $549 on 1040.