Originally Posted by clifp
My guess is your schedule D has lots of transaction enough the IRS agents eyes would glaze over at whatever the computer flagged.
That's not my experience. I missed reporting one stock sale once, and got a letter pointing out that the 1099-Bs reported didn't match my schedule D. I found the missing transaction but was still about $8K off in proceeds. I submitted the amended return with a note that if it still didn't add up would they please list the transactions they show for me so I can see what's missing. They just came back with a letter that I was still $8K short. I called and got someone to step through each one with me and she confirmed I had them all, and made a note in my case and it was finally done. The point is, the computer doesn't glaze over, it will kick it out. The agents then may glaze over but only after they have sent the bill.
That was on proceeds. The basis may be different because older transactions still aren't reported so it will be years before they expect them to completely match in most cases.
In any case, keeping a note is probably the best you can do, and it will probably be fine.