CPT code 81416: Exome sequencing, each comparator exome2026 Medicare lab fee · Clinical Laboratory Fee Schedule
Reports sequence analysis of each comparator exome, such as a relative’s exome, alongside primary exome testing for an unexplained inherited disorder.
Medicare pays $12,000.00 for 81416 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
$12,000.00
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 81416 covers
This code reports sequence analysis of one comparator exome in an exome evaluation for an unexplained constitutional or heritable disorder. A comparator is typically a relative, such as a parent or sibling, whose results help interpret the affected person’s findings. The molecular laboratory performing the analysis reports the service; the comparator’s result is evaluated in relation to the primary exome analysis.
Report one unit for each comparator exome analyzed, in addition to the primary exome service reported with 81415. The code is paid only through the Clinical Laboratory Fee Schedule. The 2026 national CLFS amount is $12,000, unchanged since 2020; one amount applies across localities, with no geographic or office-versus-facility adjustment. The physician fee schedule excludes this test by statute, so payment is through the CLFS rather than a separate physician-fee-schedule payment.
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 81416
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 81416. 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 81416 with status X (excluded by statute), so the test itself is paid only from the CLFS.
81416 on the lab fee schedule since 2020
81416 · CLFS 2026 Q4 (current)
$12,000.00
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.
81416 compared with similar tests
- 81415Exome analysisInitial sequence analysis$4,780.00
- 81415 reports the primary exome analysis. Use 81416 for each comparator exome analyzed in addition to that primary service.
- 81417Exome re-evaluationPreviously obtained sequence$320.00
- 81417 is for re-evaluating exome data; 81416 is for sequence analysis of each comparator exome.
- 81425Genome sequencingConstitutional or heritable disorders$5,031.20
- 81425 reports primary genome sequence analysis. 81416 applies to comparator exome analysis, not comparator genome analysis.
81416 billing questions
When should 81416 be reported instead of 81415?
81416 reports sequence analysis for each comparator exome, such as a relative’s. Report 81415 for the primary exome analysis; 81416 is reported in addition when comparator exomes are analyzed.
How many units are reported?
Report one unit for each comparator exome analyzed. The unit count should match the comparator exomes documented for the service.
Can 81416 be reported by itself?
It is an add-on to the primary exome analysis reported with 81415. It represents comparator analysis, not the primary exome service.
Does 81416 have a separate physician-fee-schedule payment?
No. Medicare pays this test through the CLFS; the physician fee schedule excludes it by statute.
How does Medicare pay 81416?
The CLFS uses one national amount per code across localities, without geographic or office-versus-facility adjustment. The amount has been unchanged since 2020.
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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