Why does my tax refund goes down by $640 when I enter my pre-tax HSA contribution while deductions part was already filled? Only contributed is $6,900 for 2018.

I am a 1st time HSA user. I found some answers where it suggest to wait for the next step i.e. the deductions part which was already filled for me.  I received W2c which had contribution that was missing in original W2