The employer's contribution has already been deducted from the taxable income. Whenever you see a code W in Box 12 of Form W-2, they refer to pre-tax contributions to the HSA (whether your employer made the contribution or it was your election to have some of your pay be contributed to the HSA, it is the same treatment: a pre-tax contribution). Without that contribution, your box 1 amount would have been $1000 higher. (If the contribution came from your employer, it would not have affected your income but you still could not claim a deduction because you personally did not make the contribution).
But, since the $2450 was your out-of-pocket (and therefore after-tax) contribution, you do receive a deduction for this amount.
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