Your HSA contributions are not subject to Income tax, Social Security Tax, or Medicare Tax; therefore, Boxes 1, 3, & 5 of your W2 have already been reduced by your $5,250 HSA Contributions.
On the other hand, your 401(k) contributions are not subject to Income Tax and reduce Box 1 of your W2; however, your 401(k) Contributions are subject to Social Security Tax and Medicare Tax so they are not deducted from Boxes 3 & 5 of your W2.
If this doesn't make sense or you have additional questions regarding this, please comment below so that I can assist you further.
