IRA rollover

I am confused by your question, you may also be confused.

You can make IRA contributions up to $7000 (if you are over age 50).  You must also have compensation from working.

A rollover is not considered a contribution and is not part of your $7000 annual limit.  If you did a direct rollover (direct from plan A to plan B) then enter the 1099-R and when asked what you did with it, select that you rolled it over to another qualified account.  It's perfectly OK to have a $3144 rollover from plan A to plan B and also $7000 of new contributions to plan B, because rollovers are not counted in your contribution limit.  

If you received a check from plan A, that is considered an indirect rollover.  You had 60 days to contribute it to plan B, but you must tell plan B that it is a rollover when you send them the money.  They may have a special form for you to fill out.   If you received a check for $3144 from plan A, and deposited $7000 into plan B, you can treat it as a $3144 rollover and $3856 of new contributions, as long as you completed the rollover within 60 days.  

If you did not tell plan B it was a rollover, or if you waited more than 60 days, then you don't have a rollover.  You have a taxable withdrawal from plan A, and $7000 of new contributions to plan B.  You will also owe a 10% penalty for early withdrawal from plan A unless you are over age 59-1/2.  

Please clarify your question.

• Was the 1099-R for $3,144, or was it a larger amount?
• You should indicate in the interview that a portion of the 1099-R ($7,000) amount was rolled into another qualified account.
• You do not have to post anything on your tax return for the 5498 but keep it for your records.
• What was the $3,100?
  • Was it a nondeductible contribution to the retirement account?
  • If so it should be listed on the 1099-R

I interpret this as being a $3,144 distribution from some kind of retirement account, maybe an IRA, and an independent new contribution of $7,000 to an IRA.  As it stands, no, the $7,000 deposit is not a rollover of any part of the $3,144 distribution.

If the $7,000 deposit was not made within the 60 days following the receipt of the $3,144, nothing can be done to change any part of the $7,000 to be a rollover of any part of the $3,144.  However, if the $7,000 deposit was made within those 60 days, you can potentially contact Fidelity to correct the record of the $7,000 deposit to show that it was a rollover of $3,144 plus a new contribution of $3,856, if it's of any benefit for you to do so.