Sometimes it's not worth challenging - it just depends on the procedure. The problem you'll occasionally run into, is when the procedure code has a guideline that states, "If a significant, separately identifiable E/M service is performed, it may be reported separately using modifier 25" or something along those lines. Although the guidelines are referring to problem-oriented E/M's when they have that kind of note (since it's necessary to show that the E/M went above and beyond the usual pre- and post-procedure work, and preventive visits can't be quantified on the same criteria as problem-oriented visits), the fact that the guidelines are vague in exactly which 'Evaluation and Management' services they're referring to, means that there's enough room for interpretation for a commercial payer to require you to add the 25 modifier to preventive visits, to get them to pay separately from other procedures done that day. Preventive E/M's are still evaluation and management codes, even though they're not really similar to problem-oriented codes. It's frustrating and difficult to challenge those denials, because they're basing them off of a guideline, and reading it verbatem, even though the interpretation is off base.
But the situation you have here isn't like that; you should be able to appeal this one successfully. I have a couple of questions for you, though...
How did all of this go down? Did the patient have an appointment for the procedure, and decide to have the well check done at the same time, or was it the other way around? The reason I ask, is that if the patient was scheduled for just a well check, and mentioned that they had a wart while in the office, you may be able to justify a problem oriented E/M, too.
It's going to depend on your documentation, though. If you've got a well check and problem at the same time, some elements overlap; the ones that don't, are HPI and MDM. A problem like a viral wart could potentially qualify for as high as a 99213, depending on the circumstances. Assuming your well check is documented correctly, if you've got at least 1 HPI documented, and the procedure itself is properly documented, you should have enough documentation to support reporting up to a 99213 in addition to the preventive E/M and procedure. It would require a 25 modifier, but the well check doesn't. If that's the case, I'd submit a corrected claim/appeal adding the other E/M, and explaining why it's warranted, and that it's the only E/M that's subject to a CPT guideline or NCCI edit. I'd even tell them that you only realized you had left it off, when they denied the claim. (Haha! Thanks for the reminder!) If they continue to deny the well check as needing a modifier after that, just add it and stop wasting time beating a dead horse.
If, however, the procedure was scheduled and the well check was taken care of at the same time, you wouldn't be able to add another E/M. Even though you shouldn't have to, I'd probably just go ahead and add the modifier to get it to process, but I'd let them know that you're reluctant to add it, since it's technically not correct. Sometimes, it's not worth the time and effort to fight over something that won't impact your reimbursement in the end, anyways. But if you wanted to fight it just to be right, more power to you - you're not wrong. Sorry my answer was so long...Hope that helps!
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