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LCD Reference Article Billing and Coding Article

Billing and Coding: Molecular Pathology Procedures

A57451

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Draft Articles are works in progress and not necessarily a reflection of the current billing and coding practices. Revisions to codes are carefully and thoroughly reviewed and are not intended to change the original intent of the LCD.

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General Information

Source Article ID
N/A
Article ID
A57451
Original ICD-9 Article ID
Not Applicable
Article Title
Billing and Coding: Molecular Pathology Procedures
Article Type
Billing and Coding
Original Effective Date
10/03/2018
Revision Effective Date
01/01/2024
Revision Ending Date
N/A
Retirement Date
N/A
AMA CPT / ADA CDT / AHA NUBC Copyright Statement

CPT codes, descriptions and other data only are copyright 2023 American Medical Association. All Rights Reserved. Applicable FARS/HHSARS apply.

Fee schedules, relative value units, conversion factors and/or related components are not assigned by the AMA, are not part of CPT, and the AMA is not recommending their use. The AMA does not directly or indirectly practice medicine or dispense medical services. The AMA assumes no liability for data contained or not contained herein.

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Copyright © 2023, the American Hospital Association, Chicago, Illinois. Reproduced with permission. No portion of the American Hospital Association (AHA) copyrighted materials contained within this publication may be copied without the express written consent of the AHA. AHA copyrighted materials including the UB‐04 codes and descriptions may not be removed, copied, or utilized within any software, product, service, solution or derivative work without the written consent of the AHA. If an entity wishes to utilize any AHA materials, please contact the AHA at 312‐893‐6816.

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CMS National Coverage Policy

Social Security Act (Title XVIII) Standard References:

  • Title XVIII of the Social Security Act, Section 1833(e) states that no payment shall be made to any provider of services or other person under this part unless there has been furnished such information as may be necessary in order to determine the amounts due such provider or other person under this part for the period with respect to which the amounts are being paid or for any prior period.

Article Guidance

Article Text

This Billing and Coding Article provides billing and coding guidance for Local Coverage Determination (LCD) L34519 Molecular Pathology Procedures. Please refer to the LCD for reasonable and necessary requirements.

Coding Guidance

Notice: It is not appropriate to bill Medicare for services that are not covered (as described by the entire LCD) as if they are covered. When billing for non-covered services, use the appropriate modifier.

The American Medical Association (AMA) Current Procedural Terminology (CPT) manual states molecular pathology procedures are medical laboratory procedures involving the analyses of nucleic acid to detect variants in genes that may be indicative of germline (e.g., constitutional disorders) or somatic (e.g., neoplasia) conditions, or to test for histocompatibility antigens (e.g., HLA). Given the elimination of the stacking procedure codes and the array-based evaluation codes molecular pathology codes now include all analytical services performed in the test (e.g., cell lysis, nucleic acid stabilization, extraction, digestion, amplification, and detection). (Note: molecular pathology procedure techniques, such as microbial identification using molecular pathology techniques and in situ hybridization analyses, may be described in other sections of the Pathology and Laboratory section of CPT.

Code selection is typically based on the specific gene(s) that is being analyzed. Codes that describe tests to assess for the presence of gene variants use common gene variant names. Typically, all of the listed variants would be tested. However, these lists are not exclusive. If other variants are also tested in the analysis, they would be included in the procedure and not reported separately. Full gene sequencing should not be reported using codes that assess for the presence of gene variants unless the CPT code specifically states full gene sequence in the code descriptor. In other words, you may only assign the CPT code that is described as “full gene sequence” if the test assay performed was a full gene sequence. 

Tier 2 molecular pathology procedures represent medically useful procedures that are generally performed in lower volumes than Tier 1 molecular pathology procedures (e.g., the incidence of the disease being tested is rare). They are arranged by level of technical resources and interpretive work by the physician or other qualified healthcare professional. If the analyte tested is not listed under one of the Tier 2 codes or is not represented by a Tier 1 code in CPT, use of the unlisted CPT code 81479 is required.

HCPCS code G0452 with modifier 26 should be used by pathologists when an interpretation of a molecular pathology test is performed. Non physician practitioners (e.g., PhD, scientists etc.) are not eligible to report this code, only physicians may use/bill this code. This code should not be billed without modifier 26 since it is an interpretation code only.

Documentation Requirements

  1. All documentation must be maintained in the patient's medical record and made available to the contractor upon request.
  2. Every page of the record must be legible and include appropriate patient identification information (e.g., complete name, dates of service[s]). The documentation must include the legible signature of the physician or non-physician practitioner responsible for and providing the care to the patient.
  3. The submitted medical record must support the use of the selected ICD-10-CM code(s). The submitted CPT/HCPCS code must describe the service performed.
  4. Documentation must be adequate to verify that coverage guidelines have been met. Thus, the medical record must contain documentation that the testing is expected to influence treatment of the condition toward which the testing is directed. The laboratory or billing provider must have on file the physician requisition which sets forth the diagnosis or condition that warrants the test(s). 
  5. Providers are required to code to specificity however, if CPT 81479 (unlisted molecular pathology procedure) is used the documentation must clearly identify the unique molecular pathology procedure performed. When multiple procedure codes are submitted on a claim (unique and/or unlisted) the documentation supporting each code should be easily identifiable.
  6. For molecular pathology tests, the ordering provider must provide to the laboratory copies of the signed informed consent documentation. 
  7. An Advance Beneficiary Notice of Noncoverage (ABN) is required before furnishing a beneficiary a test which the physician or laboratory believes to be noncovered as not reasonable or necessary. The physician or laboratory must obtain a signed ABN from the beneficiary (or representative) that the physician or laboratory has informed him/her on the non-coverage of the test and that there will be a charge for the test. 

Response To Comments

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Coding Information

Bill Type Codes

Code Description
999x Not Applicable
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Revenue Codes

Code Description
99999 Not Applicable
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CPT/HCPCS Codes

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Group 1

(188 Codes)
Group 1 Paragraph

Note: Providers are reminded to refer to the long descriptors of the CPT codes in their CPT book.

The following Group 1 CPT codes associated with the services outlined in this Billing and Coding Article will not have diagnosis code limitations applied at this time.

 Group 1 Codes
Code Description
81105 Hpa-1 genotyping
81106 Hpa-2 genotyping
81107 Hpa-3 genotyping
81108 Hpa-4 genotyping
81109 Hpa-5 genotyping
81110 Hpa-6 genotyping
81111 Hpa-9 genotyping
81112 Hpa-15 genotyping
81120 Idh1 common variants
81121 Idh2 common variants
81162 Brca1&2 gen full seq dup/del
81163 Brca1&2 gene full seq alys
81164 Brca1&2 gen ful dup/del alys
81165 Brca1 gene full seq alys
81166 Brca1 gene full dup/del alys
81167 Brca2 gene full dup/del alys
81170 Abl1 gene
81171 Aff2 gen aly detc abnl allel
81172 Aff2 gen alys charac alleles
81173 Ar gene full gene sequence
81174 Ar gene known famil variant
81175 Asxl1 full gene sequence
81176 Asxl1 gene target seq alys
81177 Atn1 gene detc abnor alleles
81178 Atxn1 gene detc abnor allele
81179 Atxn2 gene detc abnor allele
81180 Atxn3 gene detc abnor allele
81181 Atxn7 gene detc abnor allele
81182 Atxn8os gen detc abnor allel
81183 Atxn10 gene detc abnor allel
81184 Cacna1a gen detc abnor allel
81185 Cacna1a gene full gene seq
81186 Cacna1a gen known famil vrnt
81187 Cnbp gene detc abnor allele
81188 Cstb gene detc abnor allele
81189 Cstb gene full gene sequence
81190 Cstb gene known famil vrnt
81200 Aspa gene
81201 Apc gene full sequence
81202 Apc gene known fam variants
81203 Apc gene dup/delet variants
81204 Ar gene charac alleles
81205 Bckdhb gene
81206 Bcr/abl1 gene major bp
81207 Bcr/abl1 gene minor bp
81208 Bcr/abl1 gene other bp
81209 Blm gene
81210 Braf gene
81212 Brca1&2 185&5385&6174 vrnt
81215 Brca1 gene known famil vrnt
81216 Brca2 gene full seq alys
81217 Brca2 gene known famil vrnt
81218 Cebpa gene full sequence
81219 Calr gene com variants
81221 Cftr gene known fam variants
81222 Cftr gene dup/delet variants
81223 Cftr gene full sequence
81224 Cftr gene intron poly t
81228 Cytog alys chrml abnr cgh
81229 Cytog alys chrml abnr snpcgh
81233 Btk gene common variants
81234 Dmpk gene detc abnor allele
81235 Egfr gene com variants
81236 Ezh2 gene full gene sequence
81237 Ezh2 gene common variants
81238 F9 full gene sequence
81239 Dmpk gene charac alleles
81240 F2 gene
81241 F5 gene
81242 Fancc gene
81243 Fmr1 gen aly detc abnl allel
81244 Fmr1 gen alys charac alleles
81245 Flt3 gene
81246 Flt3 gene analysis
81248 G6pd known familial variant
81249 G6pd full gene sequence
81250 G6pc gene
81251 Gba gene
81252 Gjb2 gene full sequence
81253 Gjb2 gene known fam variants
81254 Gjb6 gene com variants
81255 Hexa gene
81256 Hfe gene
81257 Hba1/hba2 gene
81258 Hba1/hba2 gene fam vrnt
81259 Hba1/hba2 full gene sequence
81260 Ikbkap gene
81261 Igh gene rearrange amp meth
81262 Igh gene rearrang dir probe
81263 Igh vari regional mutation
81264 Igk rearrangeabn clonal pop
81265 Str markers specimen anal
81266 Str markers spec anal addl
81267 Chimerism anal no cell selec
81268 Chimerism anal w/cell select
81269 Hba1/hba2 gene dup/del vrnts
81270 Jak2 gene
81271 Htt gene detc abnor alleles
81272 Kit gene targeted seq analys
81273 Kit gene analys d816 variant
81274 Htt gene charac alleles
81275 Kras gene variants exon 2
81276 Kras gene addl variants
81277 Cytogenomic neo microra alys
81284 Fxn gene detc abnor alleles
81285 Fxn gene charac alleles
81286 Fxn gene full gene sequence
81287 Mgmt gene prmtr mthyltn alys
81288 Mlh1 gene
81289 Fxn gene known famil variant
81290 Mcoln1 gene
81291 Mthfr gene
81292 Mlh1 gene full seq
81293 Mlh1 gene known variants
81294 Mlh1 gene dup/delete variant
81295 Msh2 gene full seq
81296 Msh2 gene known variants
81297 Msh2 gene dup/delete variant
81298 Msh6 gene full seq
81299 Msh6 gene known variants
81300 Msh6 gene dup/delete variant
81301 Microsatellite instability
81302 Mecp2 gene full seq
81303 Mecp2 gene known variant
81304 Mecp2 gene dup/delet variant
81305 Myd88 gene p.leu265pro vrnt
81307 Palb2 gene full gene seq
81308 Palb2 gene known famil vrnt
81309 Pik3ca gene trgt seq alys
81310 Npm1 gene
81311 Nras gene variants exon 2&3
81312 Pabpn1 gene detc abnor allel
81313 Pca3/klk3 antigen
81314 Pdgfra gene
81315 Pml/raralpha com breakpoints
81316 Pml/raralpha 1 breakpoint
81317 Pms2 gene full seq analysis
81318 Pms2 known familial variants
81319 Pms2 gene dup/delet variants
81320 Plcg2 gene common variants
81321 Pten gene full sequence
81322 Pten gene known fam variant
81323 Pten gene dup/delet variant
81324 Pmp22 gene dup/delet
81325 Pmp22 gene full sequence
81326 Pmp22 gene known fam variant
81327 Sept9 gen prmtr mthyltn alys
81329 Smn1 gene dos/deletion alys
81330 Smpd1 gene common variants
81331 Snrpn/ube3a gene
81332 Serpina1 gene
81333 Tgfbi gene common variants
81334 Runx1 gene targeted seq alys
81336 Smn1 gene full gene sequence
81337 Smn1 gen nown famil seq vrnt
81340 Trb@ gene rearrange amplify
81341 Trb@ gene rearrange dirprobe
81342 Trg gene rearrangement anal
81343 Ppp2r2b gen detc abnor allel
81344 Tbp gene detc abnor alleles
81345 Tert gene targeted seq alys
81349 Cytog alys chrml abnr lw-ps
81361 Hbb gene com variants
81362 Hbb gene known fam variant
81363 Hbb gene dup/del variants
81364 Hbb full gene sequence
81400 Mopath procedure level 1
81401 Mopath procedure level 2
81402 Mopath procedure level 3
81403 Mopath procedure level 4
81404 Mopath procedure level 5
81405 Mopath procedure level 6
81443 Genetic tstg severe inh cond
81479 Unlisted molecular pathology
81523 Onc brst mrna 70 cnt 31 gene
0111U Onc colon ca kras&nras alys
0129U Hered brst ca rltd do panel
0130U Hered colon ca do mrna pnl
0153U Onc breast mrna 101 genes
0154U Onc urthl ca rna fgfr3 gene
0155U Onc brst ca dna pik3ca gene
0156U Copy number sequence alys
0157U Apc mrna seq alys
0158U Mlh1 mrna seq alys
0159U Msh2 mrna seq alys
0160U Msh6 mrna seq alys
0161U Pms2 mrna seq alys
0162U Hered colon ca trgt mrna pnl
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CPT/HCPCS Modifiers

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 Group 1 Codes

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ICD-10-CM Codes that Support Medical Necessity

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(1 Code)
Group 1 Paragraph

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 Group 1 Codes
Code Description
XX000 Not Applicable
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ICD-10-CM Codes that DO NOT Support Medical Necessity

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(1 Code)
Group 1 Paragraph

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 Group 1 Codes
Code Description
XX000 Not Applicable
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ICD-10-PCS Codes

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Group 1 Paragraph

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 Group 1 Codes

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Additional ICD-10 Information

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Bill Type Codes

Contractors may specify Bill Types to help providers identify those Bill Types typically used to report this service. Absence of a Bill Type does not guarantee that the article does not apply to that Bill Type. Complete absence of all Bill Types indicates that coverage is not influenced by Bill Type and the article should be assumed to apply equally to all claims.

Code Description
999x Not Applicable
N/A

Revenue Codes

Contractors may specify Revenue Codes to help providers identify those Revenue Codes typically used to report this service. In most instances Revenue Codes are purely advisory. Unless specified in the article, services reported under other Revenue Codes are equally subject to this coverage determination. Complete absence of all Revenue Codes indicates that coverage is not influenced by Revenue Code and the article should be assumed to apply equally to all Revenue Codes.

Code Description
99999 Not Applicable
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Other Coding Information

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Group 1

Group 1 Paragraph

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 Group 1 Codes

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Coding Table Information

Excluded CPT/HCPCS Codes - Table Format
Code Descriptor Generic Name Descriptor Brand Name Exclusion Effective Date Exclusion End Date Reason for Exclusion
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Non-Excluded CPT/HCPCS Ended Codes - Table Format
Code Descriptor Generic Name Descriptor Brand Name Exclusion Effective Date Exclusion End Date Reason for Exclusion
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Revision History Information

Revision History Date Revision History Number Revision History Explanation
01/01/2024 R10

Article revised and published on 01/25/2024 effective for dates of service on and after 01/01/2024 to reflect the Annual HCPCS/CPT Code Updates. For the following Group 1 CPT codes the long description was changed: 81171, 81172, 81243, 81244, 81403, 81404. Depending on which description is used in this article, there may not be any change in how the code displays. 
01/01/2023 R9

Article revised and published on 01/26/2023 effective for dates of service on and after 01/01/2023 to reflect the Annual HCPCS/CPT Code Updates. For the following CPT code either the short description and/or the long description was changed. Depending on which description is used in this article, there may not be any change in how the code displays: 81330 in Group 1 Codes.
01/01/2022 R8

Article revised and published on 01/20/22 effective for dates of service on and after 01/01/2022 to reflect the Annual HCPCS/CPT Code Updates. The following CPT codes have been added to the ‘CPT/HCPCS Codes’ section for ‘Group 1 Codes’: 81349 and 81523. For the following CPT codes either the short description and/or the long description was changed. Depending on which description is used in this article, there may not be any change in how the code displays: 81228, 81229, 81405, 0154U, and 0155U in the ‘CPT/HCPCS Codes’ section for ‘Group 1 Codes’.
12/12/2021 R7

Article revised and published on 12/09/2021 effective for dates of service on and after 12/12/2021. Removed the following CPT codes from the “CPT/HCPCS Codes/Group 1 Codes:” section of the billing and coding article: 81220, 81225, 81226, 81227, 81230, 81231, 81232, 81247, 81283, 81306, 81328, 81335, 81346, 81350, 81355, 81406, 81407, and 81408.

For Pharmacogenomics testing services, please see the new LCD L39073 and related billing and Coding Article A58812 for Pharmacogenomics Testing effective for dates of service on and after 12/12/2021.

Minor formatting changes have been made throughout the article.
01/01/2021 R6

Article revised and published on 02/11/2021 effective for dates of service on and after 01/01/2021 to reflect the annual CPT code updates. The following CPT codes have descriptor changes: 81206, 81207, 81266, 81267, 81268, 81288, 81401, 81402, 81403, 81404, 81405, 0154U, and 0155U. Minor formatting changes have been made throughout the article.
10/01/2020 R5

Article revised and published on 10/29/2020 effective for dates of service on and after 10/01/2020 to that the following CPT code has undergone a long descriptor change: Group 1 Codes: 0154U. In addition, formatting changes were made throughout the article. (PITL # 2020PITLAB007).
04/01/2020 R4

Explanation of revision: Removed CPT codes 0154U and 0155U from the “CPT/HCPCS Codes/Group 1 Paragraph:” section of the billing and coding article, as the revised descriptor for CPT codes 0154U and 0155U is available in the “CPT/HCPCS Codes/Group 1 Codes:” section of the billing and coding article.
04/01/2020 R3

Revision Number: 3
Publication: April 2020 Connection
LCR A/B2020-027

Explanation of Revision: Based on CR 11550, 11680, 11681, and 11691 (April 2020 Quarterly Updates), the “CPT/HCPCS Codes/Group 1 Codes:” section of the Billing and Coding article was updated to revise the descriptors for CPT codes 0154U and 0155U. The effective date of this revision is based on date of service.
01/01/2020 R2

Revision Number: 2
Publication: December 2019 Connection
LCR A/B2020-001

Explanation of Revision: Annual 2020 HCPCS Update. Descriptor revised for CPT codes 81350, 81404, 81406, and 81407. In addition, added CPT codes 0153U, 0154U, 0155U, 0156U, 0157U, 0158U, 0159U, 0160U, 0161U, 0162U, 81277, 81307, 81308, and 81309. The effective date of this revision is based on date of service.
10/01/2019 R1

Moved HCPCS codes 0111U, 0129U, and 0130U from the “CPT/HCPCS Codes/Group 1 Paragraph:” section of the Billing and Coding article to the “CPT/HCPCS Codes/Group 1 Codes:” section of the Billing and Coding article.
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LCDs
L34519 - Molecular Pathology Procedures
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