HSA contribution calculation on Form 8889 not generating a deduction

doing my girfriends taxes (single filer). her W2 shows $7000 in box 12A with code W

 

when Turbo tax completes form 8889, I do not see this $7000 transfer as a deduction to 1040 Schedule 1.

 

its my understanding that the $7k was taken out of her paychecks 'after tax' .. in other words, her wages in box 1 of W2 include that $7k and thats why I was expecting to see the deduction on 1040.