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    v1.0.28
    OpenPayerBilling CodesGenetic Analysis ProceduresCPT cpt-81206-bcr-abl1-major-breakpoint-molecular-test
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    CPT 81206: BCR-ABL1 Major Breakpoint Fusion Gene Analysis

    CPT code 81206 describes laboratory testing to detect and/or quantify the major breakpoint BCR/ABL1 fusion gene on chromosome 22 resulting from a translocation; this represents a molecular genetic test performed by a clinical laboratory as a qualitative or quantitative assay to identify the presence and amount of the BCR/ABL1 fusion transcript, typically provided as a molecular diagnostic service in a hospital or reference laboratory setting (clinical molecular pathology/molecular diagnostics).

    For related coverage guidance, see recent payer policy updates: RTM Testing of Homocysteine Metabolism-Related Conditions, Multimarker Serum Testing Related to Ovarian Cancer, Genomic Profiling for Selecting Targeted Cancer Therapies.

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    Clinical & Coding Specifications

    Clinical Context

    A typical patient is an adult with suspected or confirmed chronic myeloid leukemia (CML) or another myeloproliferative neoplasm being evaluated for the BCR-ABL1 fusion gene. The clinician (hematologist/oncologist) orders molecular testing to detect and/or quantify the BCR-ABL1 major breakpoint transcript to: confirm diagnosis, establish baseline disease burden, or monitor response to tyrosine kinase inhibitor therapy. A peripheral blood or bone marrow specimen is collected in the outpatient clinic or inpatient ward and sent to a molecular pathology laboratory. The laboratory performs qualitative reverse-transcription PCR to identify the presence of the BCR-ABL1 fusion and/or quantitative real-time PCR to measure transcript level (e.g., international scale percent or copy number) for longitudinal monitoring. Results are returned to the ordering provider and used to guide diagnosis, risk stratification, and treatment decisions.

    Related CPT Codes

    CPT CodeDescriptionRelationship to This Procedure
    81206BCR-ABL1 (major breakpoint) gene sequence analysis; qualitative or quantitativePrimary molecular test to detect/measure the BCR-ABL1 fusion transcript for diagnosis and monitoring of CML.
    80750Sequence analysis; DNA, any method, 1-250 bp (eg, sequencing of small targets)May be used in laboratories for confirmatory sequencing of breakpoints or variant characterization when needed.
    88240Flow cytometry, single tumor marker, each markerOften performed alongside molecular testing to characterize immunophenotype in leukemias at diagnosis.
    88182Cytogenetic studies, fluorescent in situ hybridization (FISH) for single probeFISH for BCR-ABL translocation is commonly performed in parallel for cytogenetic confirmation.
    81207BCR-ABL1 (minor breakpoint) gene sequence analysis; qualitative or quantitativeRelated molecular assay for alternative BCR-ABL1 breakpoints that may be ordered if major breakpoint testing is negative but suspicion remains.

    Related Modifiers

    8 rows

    ModifierDescriptionWhen to Use
    26Modifier 26 (Professional Component) identifies and bills only the professional portion of a split service — the physician’s interpretation, report, and medical judgment — when the technical…- Use CPT Modifier -26 when you are billing only the professional component (PC) of a split‑bill eligible service—i.e., you performed the physician interpretation, medical judgment and prepared a…
    90Modifier ‑90 (Reference/Outside Laboratory) indicates that a laboratory test was performed by an entity other than the treating or reporting provider. The American Medical Association defines…- Use CPT modifier -90 when a laboratory test is performed by an outside/reference laboratory (an entity other than the treating or reporting physician or qualified professional) and the claim needs…
    91Modifier 91 — “Repeat Clinical Diagnostic Laboratory Test” — is appended when the exact same CPT laboratory test is performed more than once for the same patient on the same day because serial,…- Use modifier 91 when the exact same CPT laboratory test is performed more than once on the same patient on the same date because serial or repeated testing is medically necessary to monitor…
    59Modifier 59 indicates a distinct procedural service when two procedures that are not normally billed together are clinically and procedurally separate. The CPT definition (as reiterated by CMS)…- Use modifier -59 to report a distinct procedural service when documentation supports that the procedure reported is not normally billed together with another service on the same day because of a…
    52Modifier ‑52 (Reduced Services) indicates that a service or procedure was partially reduced or omitted at the provider’s discretion, allowing reporting of the basic procedure number with a qualifier…- Use modifier -52 when a physician or qualified health professional electively reduces or omits part of a procedure or service (for example, performing fewer required views or omitting a portion of…
    53Modifier 53 (Discontinued Procedure) signals that a surgical or diagnostic service was begun by the physician but terminated because of extenuating circumstances that threatened the patient’s…- Use modifier -53 when a physician/qualified healthcare professional has started a surgical or diagnostic procedure (e.g., anesthesia administered, incision or scope insertion) and then discontinues…
    76Modifier -76, Repeat Procedure or Service by Same Physician or Other Qualified Health Care Professional, is appended when the same provider performs an identical, medically necessary procedure or…- Use modifier -76 when the same physician or other qualified health care professional performs an identical procedure or service a second (or subsequent) time on the same date of service and the…
    62Modifier 62 indicates that two surgeons function as co‑surgeons, each performing distinct parts of the same primary surgical procedure. It is appended to the primary procedure code (and any…- Use modifier -62 when two surgeons act as co‑surgeons (both primary surgeons) on a single definitive primary procedure, each performing distinct parts of the same surgical procedure (append -62 to…

    Related Provider Taxonomies

    8 rows

    Taxonomy CodeSpecialtyNotes
    207RH0000XHematology (Internal Medicine) PhysicianAn internist with additional training who specializes in diseases of the blood, spleen and lymph. This specialist treats conditions such as anemia, cl…
    207L00000XAnesthesiology PhysicianAn anesthesiologist is trained to provide pain relief and maintenance, or restoration, of a stable condition during and immediately following an opera…
    363L00000XNurse Practitioner(1) A registered nurse provider with a graduate degree in nursing prepared for advanced practice involving independent and interdependent decision mak…
    207K00000XAllergy & Immunology PhysicianAn allergist-immunologist is trained in evaluation, physical and laboratory diagnosis, and management of disorders involving the immune system. Select…
    364S00000XClinical Nurse SpecialistA registered nurse who, through a graduate degree program in nursing, or through a formal post-basic education program or continuing education courses…
    207PE0004XEmergency Medical Services (Emergency Medicine) PhysicianAn emergency medicine physician who specializes in non-hospital based emergency medical services (e.g., disaster site, accident scene, transport vehic…
    163WR0400XRehabilitation Registered NurseNursing Service Providers · Registered Nurse
    208600000XSurgery PhysicianA general surgeon has expertise related to the diagnosis - preoperative, operative and postoperative management - and management of complications of s…

    Related Payer Policy Updates

    Specialty: Genetic & Molecular Testing1 / 3

    10 rows

    PolicyPayerEffective Date
    RTM Testing of Homocysteine Metabolism-Related ConditionsOscar Health2026-10-01
    Multimarker Serum Testing Related to Ovarian CancerBlue Cross Blue Shield - Rhode Island2026-09-01
    Genomic Profiling for Selecting Targeted Cancer TherapiesBlue Cross Blue Shield - Rhode Island2026-09-01
    Whole Exome and Whole Genome Sequencing for Diagnosis of Genetic DisordersBlue Cross Blue Shield - Rhode Island2026-09-01
    Biomarker and Genetic/Molecular Testing Coverage and Prior AuthorizationBlue Cross Blue Shield - Rhode Island2026-09-01
    Non-Invasive Prenatal Testing (NIPT)univerahealthcare2026-08-17
    Lumizyme (alglucosidase alfa) — Pompe Disease (acid alpha‑glucosidase deficiency)Cigna2026-08-15
    Molecular Oncology Testing for Solid Tumor Cancer Diagnosis, Prognosis, and Treatment DecisionsColorado Rocky Mountain Health Plans2026-08-01
    Carrier Testing Panels for Genetic DiseasesColorado Rocky Mountain Health Plans2026-08-01
    Molecular Oncology Testing for Hematologic Cancer Diagnosis, Prognosis, and Treatment DecisionsColorado Rocky Mountain Health Plans2026-08-01

    Related Codes

    CPT-81105-HPA-1-PLATELET-ANTIGEN-1-GENOTYPING-ITGB3-CD61

    CPT 81105: HPA-1 (ITGB3/CD61) Genotyping, Technical Component

    CPT-81106-HPA-2-T145M-GENETIC-ALLELE-ANALYSIS

    CPT 81106: HPA-2 (T145M) Platelet Antigen Genotyping

    CPT-81107-HPA-3-GENETIC-ANALYSIS-TECHNICAL-COMPONENT

    CPT 81107: HPA‑3 (I843S) Platelet Antigen Genotyping

    CPT-81108-HPA-4-R143Q-GENOTYPING

    CPT 81108: HPA-4 (R143Q) Genotyping

    CPT-81109-HPA-5-K505E-GENETIC-ANALYSIS

    CPT 81109: HPA-5 (K505E) Genotyping Test

    CPT-81110-HPA-6-R489Q-GENOTYPING

    CPT 81110: HPA-6 (R489Q) Genotyping, Technical Component

    CPT-81111-HPA-9-V837M-ALLELE-ANALYSIS

    CPT 81111: HPA-9 (V837M) Genotyping, Technical Test

    CPT-81112-HPA-15-GENETIC-ANALYSIS-S682Y

    CPT 81112: HPA-15 (S682Y) Platelet Antigen Genotyping

    CPT-81120-IDH1-MOLECULAR-DIAGNOSTIC-TEST

    CPT 81120: IDH1 Mutation Detection, Technical Component

    CPT-81121-IDH2-MOLECULAR-DIAGNOSTIC-TEST

    CPT 81121: IDH2 Mutation Detection, Technical Component

    Showing 1–10 of 199

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    Frequently Asked Questions

    References

    1. 1.CPT® Codes and Descriptions. AAPC. Retrieved Aug 11, 2026.Maintains the CPT code set's official descriptions and guidelines, licensed from the American Medical Association, used as the definitional source for CPT codes on this page.
    2. 2.HCPCS Quarterly Update. Centers for Medicare & Medicaid Services (CMS). Retrieved Aug 11, 2026.CMS's quarterly release of HCPCS Level II codes and short/long descriptors, the source for HCPCS code definitions and update history.
    3. 3.ICD-10-CM Full Code List. Centers for Medicare & Medicaid Services (CMS). Retrieved Aug 11, 2026.CMS's complete ICD-10-CM diagnosis code list, used to cross-reference diagnosis codes associated with this procedure or service.
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