PENALTY-Capital loss carryover

Probably not, but you should file an amended return right away (with a corrected schedule D attached) before you do get audited - and you can be sure that you will get audited but it could take a year or more.

If the capital gains was reported on a 1099 form, the IRS's computers will eventually match that against your return and you will receive a computer generated letter asking you to explain the difference (audit).

There won't be a penalty, because if you did get a CP2501 letter, you would use up $1000 of the unclaimed capital loss carryover. However, you should file an amended return (but no rush on it, meaning you can take 3 months to do it) because:

(1) So your capital loss carryover to the following year is correct. In reality your capital loss carryover to the next year is $5000 but in your original return you have it as $6000. If in your 2008 tax return you use up the $6000, then when you get the CP2501 letter for your 2007 return, you will write back with an amended return claiming an additional $1000 gain on Schedule D (which is what the CP2501 letter is for), but you will also use up an additional $1000 of your capital loss carryover. But then on your 2008 return you might owe interest because you claimed $6000 capital loss but should have claimed $5000. So basically, get your accounting straight before the end of 2008 just to save hassle down the road.

(2) So you don't have to deal with the CP2501.