CPT code 81297: MSH2 analysis, duplication and deletion variants2026 Medicare lab fee · Clinical Laboratory Fee Schedule
MSH2 duplication and deletion analysis evaluates gene-level changes associated with Lynch syndrome during an inherited colorectal and other cancer risk workup.
Medicare pays $213.30 for 81297 under the 2026 Clinical Laboratory Fee Schedule: one national amount, the same in every state and setting.
Medicare lab fee · CLFS 2026 Q4
National CLFS amount
$213.30
In effect since Jan 1, 2026. The same amount in every state, payment locality and setting.
- Geographic adjustment
- None
- Office vs facility
- Same
- Since 2020
- Unchanged
- CMS updates
- Quarterly
Medicare pays the lesser of the lab’s charge and this amount. Patients usually owe no Part B deductible or coinsurance for covered clinical lab tests.
On this page 8 sections
What 81297 covers
This molecular genetic test evaluates the MSH2 gene for duplications or deletions. These gene-level changes can be associated with Lynch syndrome, an inherited cancer predisposition. Oncologists, gastroenterologists, and genetics professionals may order the analysis when personal or family history, or tumor findings, raise concern for Lynch syndrome. Clinical molecular laboratories perform and report the testing.
Report 81297 for MSH2 duplication or deletion analysis, rather than full-gene sequencing or testing for known MSH2 variants, which have separate codes. Medicare pays this test only through the CLFS. The 2026 national CLFS amount is $213.30, unchanged from 2020 through 2026. The same amount applies in every state and locality, with no office or facility payment difference.
This summary was written with AI assistance from CMS Clinical Laboratory Fee Schedule data. Amounts on this page come directly from CMS files.
How Medicare pays 81297
Clinical lab tests aren’t priced like physician services. They’re paid from their own fee schedule, with its own rules. See the whole lab fee schedule.
One national amount
CMS sets a single Clinical Laboratory Fee Schedule amount for 81297. There’s no geographic (GPCI) adjustment, so it pays the same in every state and payment locality.
No office or facility rate
Lab tests aren’t built from relative value units, so there’s no office and facility split: the place of service doesn’t change the CLFS amount.
Updated every quarter
CMS republishes the CLFS each quarter. New tests, often proprietary laboratory analyses (PLA codes), join during the year; existing amounts are updated each January.
Excluded from the physician fee schedule
The physician fee schedule lists 81297 with status X (excluded by statute), so the test itself is paid only from the CLFS.
81297 on the lab fee schedule since 2020
81297 · CLFS 2026 Q4 (current)
$213.30
Unchanged since Jan 1, 2020
27 quarterly CLFS releases on file, first CLFS 2020 Q1. A code missing from a quarter wasn’t on that release.
81297 compared with similar tests
- 81295MSH2 testingFull gene sequence$381.70
- 81295 is for full-gene MSH2 sequencing. Use 81297 when the analysis targets MSH2 duplications or deletions.
- 81296MSH2 testingKnown familial variants$337.73
- 81296 tests for known MSH2 variants. 81297 addresses duplications or deletions in MSH2.
- 81294MLH1 analysisDuplication and deletion variants$202.40
- 81294 addresses MLH1 duplications or deletions, while 81297 addresses the corresponding type of analysis in MSH2.
81297 billing questions
When should 81297 be selected instead of 81295 or 81296?
Use 81297 for MSH2 duplication or deletion analysis. Code 81295 describes full-gene sequencing, while 81296 is for testing known MSH2 variants.
Does this code cover MSH2 sequencing as well as copy-number changes?
No. 81297 identifies duplication or deletion analysis; full-gene sequencing and testing for known variants are represented by separate codes.
How does Medicare pay for 81297?
Medicare pays 81297 only under the CLFS. Its national amount is the same across localities and settings.
What should the laboratory report support?
Documentation should identify the MSH2 duplication or deletion analysis performed. It should distinguish that work from full-gene sequencing or known-variant testing.
Where this amount comes from
FeeBase reads lab amounts directly from the CMS Clinical Laboratory Fee Schedule file for the quarter: one row per code, with its payment indicator and national amount. Contractor-priced tests are labeled, never given a made-up amount. Amounts are Medicare payment limits, not a patient’s bill or a commercial rate.
CMS CLFS 2026 Q4 · effective Oct 1, 2026 through the day before Jan 1, 2027
Show the CMS file line behind this amount
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