Schedule D stocks losses & sale of primary residence issue

[Ghost-Tax]

Hi all and again thank you in advance for reading this and hopefully helping me out.

To generalize this let's say there was a loss of 100k from stocks. Then a Home Sale was completed to which resulted a capital gain for the primary residence of 1,000,000. Married filing jointly 500k so taxable capital gain of 500k. Schedule D automatically subtracts the whole 100k loss from stocks and results in a 400k capital gain instead of the 497k (3k/year net capital loss from stock). 

Can anyone help?

[IRonMaN · Accepted solution]

Nothing to help with, it is handling the sales correctly.  $3000 per year only applies if there are no gains to offset.

[Ghost-Tax]

Ok thanks. I never had this scenario and I just didn't know. Thank you again.

[IRonMaN]

You betcha!