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    v1.0.30
    OpenPayerBilling CodesCytogenetic StudiesCPT cpt-88248-chromosome-analysis-breakage-syndrome
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    CPT 88248: Chromosome Analysis for Breakage Syndromes

    CPT code 88248 describes a laboratory chromosome analysis for suspected breakage syndromes (for example, Fanconi anemia, ataxia telangiectasia, fragile X) in which the lab analyst reviews and scores 50 to 100 cells, counts 20 cells, and prepares two karyotypes; the service is a cytogenetic analysis typically performed by a clinical laboratory or cytogenetics laboratory and is usually provided in an outpatient laboratory or hospital laboratory setting.

    For related coverage guidance, see recent payer policy updates: Oral Cancer Screening and Testing, RTM Testing for Alpha-1 Antitrypsin Deficiency, Cytochrome P450 Genotype-Guided Treatment Strategy Corporate Medical Policy.

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    Clinical & Coding Specifications

    Clinical Context

    A pediatric hematology clinic evaluates a 6-year-old child with progressive pancytopenia, short stature, and recurrent infections. The clinician orders a cytogenetic breakage study to assess for Fanconi anemia. A laboratory receives the peripheral blood specimen, cultures lymphocytes, treats with diepoxybutane (DEB) or mitomycin C to induce chromosomal breakage, and the cytogenetics technologist performs 88248 by scoring 50–100 cells, counting 20 metaphases for breakage, and preparing two karyotypes. Results are reviewed by a board‑certified clinical cytogeneticist who issues the final report to the ordering hematologist. Typical site of service is a hospital outpatient laboratory or independent clinical cytogenetics laboratory supporting outpatient and inpatient specimens. Common clinical indications include suspected Fanconi anemia, ataxia‑telangiectasia, and fragile X syndrome when chromosomal breakage testing is required to evaluate genomic instability.

    Related CPT Codes

    CPT CodeDescriptionRelationship to This Procedure
    88248Chromosome analysis for breakage syndrome; scoring 50–100 cells, count 20 cells, prepare two karyotypesPrimary procedure for detecting chromosomal breakage associated with Fanconi anemia, ataxia‑telangiectasia, and other instability syndromes.
    88240Chromosome analysis; per cell culture, general chromosome study, limited number of cells (e.g., 5–20 cells)Often performed when a limited or preliminary karyotype is required or when specimen quality limits yield; may precede or follow 88248 if additional analysis is needed.
    88241Chromosome analysis; study of 20–50 cellsUsed for intermediate cell counts when full breakage scoring at 88248 thresholds is not indicated or feasible.
    88271Fluorescence in situ hybridization (FISH) or other cytogenetic adjunct testingFISH may be performed alongside to detect specific chromosomal abnormalities or to corroborate breakage patterns.
    88262Chromosome analysis; tissue culture, bone marrow or blood, complete evaluationMay be billed for comprehensive cytogenetic evaluation including culture and analysis beyond breakage‑specific studies.

    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…
    22Modifier –22 (Increased Procedural Services) is used when a reported procedure is substantially more extensive than normally required. The CPT Manual and CMS state it may be appended only when the…- When to use: Append modifier -22 to a procedural CPT code when the service performed is substantially more extensive than the usual service described by that code — i.e., the procedure required…
    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…
    78CPT modifier -78 indicates an unplanned, related return to the operating or procedure room by the same provider during the global postoperative period. It is appended when treatment for a…- Use modifier -78 when an unplanned, related complication during the original procedure’s global postoperative period requires the patient to return to a formal operating or procedure room and the…

    Related Provider Taxonomies

    8 rows

    Taxonomy Code
    207RC0000X
    207RP1001X
    207Q00000X
    208D00000X
    2080P0208X
    261QS0132X
    207LP2900X
    101YP1600X

    Related ICD-10-CM Codes

    23 rows

    ICD-10-CM CodeDescription
    D61.82Myelophthisis
    D62Acute posthemorrhagic anemia
    D64.9Anemia, unspecified
    D70.9Neutropenia, unspecified
    D75.81Myelofibrosis
    D84.9Immunodeficiency, unspecified
    F70Mild intellectual disabilities
    F84.0Autistic disorder
    G11.3Cerebellar ataxia with defective DNA repair
    G11.4Hereditary spastic paraplegia

    Showing 1–10 of 23

    Related Payer Policy Updates

    Specialty: Genetic & Molecular Testing1 / 3

    10 rows

    PolicyPayerEffective Date
    Oral Cancer Screening and TestingOscar Health2027-01-01
    RTM Testing for Alpha-1 Antitrypsin DeficiencyOscar Health2027-01-01
    Cytochrome P450 Genotype-Guided Treatment Strategy Corporate Medical Policybcbsvermont2027-01-01
    Carrier Testing Panels for Genetic Diseases (for Kentucky Only)UnitedHealthcare2026-10-01
    Genetic Testing for Neurological Disorders (for Kansas Only)UnitedHealthcare2026-10-01
    Genetic and Molecular TestingProvidence Health Plan2026-10-01
    Cell-Free Fetal DNA Testing (for Idaho Only)UnitedHealthcare2026-10-01
    Next Generation Sequencing for Minimal Residual Disease DetectionProvidence Health Plan2026-10-01
    Pharmacogenetic Panel Testing (for Kansas Only)UnitedHealthcare2026-10-01
    Non-Covered Genetic Panel TestsProvidence Health Plan2026-10-01

    Related Codes

    CPT-88230-LYMPHOCYTE-TISSUE-CULTURE-NONNEOPLASTIC-DISORDER

    CPT 88230: Lymphocyte Culture for Nonneoplastic Disorder

    CPT-88233-TISSUE-CULTURE-SKIN-SOLID-TISSUE-NONNEOPLASTIC

    CPT 88233: Tissue Culture for Nonneoplastic Disorders

    CPT-88235-AMNIOTIC-FLUID-CHORIONIC-VILLUS-TISSUE-CULTURE

    CPT 88235: Tissue Culture Preparation from Amniotic Fluid or Chorionic Villi

    CPT-88237-BONE-MARROW-BLOOD-CELL-CULTURE-NEOPLASTIC-DISORDER

    CPT 88237: Cell Culture for Neoplastic Disorders

    CPT-88239-SOLID-TUMOR-CELL-CULTURE-NEOPLASTIC-DISORDER

    CPT 88239: Cell Culture From Solid Tumor for Neoplastic Disorder

    CPT-88240-CELL-LINE-CRYOPRESERVATION-STORAGE

    CPT 88240: Cryopreservation and Storage of Cell Line

    CPT-88241-THAW-AND-EXPAND-FROZEN-CELLS-SINGLE-ALIQUOT

    CPT 88241: Thaw and Expand Previously Frozen Cells, Single Aliquot

    CPT-88245-CHROMOSOME-ANALYSIS-SISTER-CHROMATID-EXCHANGE-SCE

    CPT 88245: Chromosome Analysis for Sister Chromatid Exchange

    CPT-88249-CHROMOSOME-ANALYSIS-BREAKAGE-SYNDROME-CLASTOGEN-STRESS

    CPT 88249: Chromosome Analysis for Breakage Syndrome, 100-Cell Clastogen Test

    CPT-88261-CHROMOSOME-ANALYSIS-KARYOTYPE-BANDING

    CPT 88261: Chromosome Analysis, Karyotype with Banding

    Showing 1–10 of 26

    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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