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    v1.0.30
    OpenPayerBilling CodesGenomic Sequencing Procedures and Other Molecular Multianalyte AssaysCPT cpt-81415-exome-sequence-analysis-unexplained-disorder
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    CPT 81415: Exome Sequence Analysis for Unexplained Disorder

    Commercial payers pay $4572 on average nationally for this procedure.

    CPT code 81415 describes an exome gene sequence analysis performed by a laboratory analyst to identify genetic variants that may explain an unexplained disorder or syndrome; the service is diagnostic genetic sequencing typically performed in a clinical molecular genetics laboratory and billed for ambulatory outpatient or specialty genetics clinic settings where comprehensive exome sequencing is indicated.

    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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    National Reimbursement Benchmarks

    National commercial rates for CPT 81415 center on BUCA’s mean commercial rate of $4,572.10, which provides a useful midpoint for market comparisons. Blue Cross Blue Shield has the highest dispersion between its 25th and 75th percentiles ($5,427.50 - $3,798.30 = $1,629.20), indicating wider variability in allowed commercial rates, while Aetna’s interquartile spread ($3,824.00 - $1,000.00 = $2,824.00) is even larger, reflecting substantial skew from low-percentile contracts to high outliers.

    UnitedHealth Group shows a tighter middle distribution with an IQR of $4,780.00 - $2,007.60 = $2,772.40, and Cigna’s interquartile range is $6,177.50 - $2,444.90 = $3,732.60, the widest of the listed payers. Overall, BUCA’s mean at $4,572.10 sits near the center of commercial market rates, while payer-specific IQRs highlight material differences in how concentrated allowed amounts are across insurers.

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    National Payer Mean Reimbursement Rates

    State Reimbursement Rates

    State: Alaska1 / 51

    Rate by payer

    Clinical & Coding Specifications

    Clinical Context

    A 5-year-old child presents to a pediatric genetics clinic with global developmental delay, multiple congenital anomalies including short stature and dysmorphic facies, and a history of unexplained metabolic testing abnormalities. Prior targeted panels (single-gene testing) and chromosomal microarray returned nondiagnostic results. The clinician orders a clinical exome sequencing test (CPT 81415) to evaluate for single-nucleotide variants or small indels across coding regions that could explain the child’s phenotype. The workflow includes genetic counseling, informed consent with discussion of diagnostic yield and secondary findings, collection of blood specimens from the proband (and often parents for trio analysis when available), sample accessioning and DNA extraction in the molecular laboratory, exome capture and high-throughput sequencing, bioinformatic alignment and variant calling, variant annotation and filtering against phenotype-driven gene lists, laboratory analyst review and interpretation, and a final report delivered to the ordering provider and genetic counselor. Results may prompt confirmatory testing, cascade testing of family members, clinical management changes, or referral to subspecialties such as endocrinology or neurology.

    Related CPT Codes

    CPT CodeDescriptionRelationship to This Procedure
    81416Exome; sequence analysis, each comparator exomePerformed when comparing additional exomes (for example, trio or multiple family members) where billing each comparator exome is required.

    Related Modifiers

    9 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…
    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…
    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…
    80CPT® Modifier 80 (Assistant Surgeon) is appended to a surgical CPT code when a physician (MD or DO) provides full, continuous assistance throughout the operative procedure. It is intended only for…- Use CPT Modifier -80 when a physician (MD or DO) serves as an assistant surgeon and provides full, continuous assistance throughout the entire operative procedure; append -80 to the surgical CPT…
    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…
    95Modifier 95 indicates that a service was provided via synchronous, real‑time audio‑video telehealth rather than in‑person. Per CMS, AAPC and professional associations, append modifier 95 to claim…- Use modifier 95 to indicate a service was furnished via synchronous, real‑time audiovisual telehealth (a live audio‑video conference between patient and provider) rather than in‑person. - Pair…

    Related Provider Taxonomies

    8 rows

    Taxonomy Code
    207SG0201X
    207SG0203X
    207SG0202X
    2083X0100X
    364SL0600X
    2471C1106X
    163WH0500X
    163WX1100X

    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-81410-GENOMIC-PANEL-AORTIC-DISEASE

    CPT 81410: Heritable Thoracic Aortic Disease Targeted Gene Panel

    CPT-81411-GENETIC-DUPLICATION-DELETION-PANEL-AORTIC-DISEASE

    CPT 81411: Genetic Panel for Aortic Dysfunction Copy Number Analysis

    CPT-81412-ASHKENAZI-JEWISH-GENOMIC-SEQUENCE-PANEL

    CPT 81412: Ashkenazi Jewish–Associated Genetic Sequence Panel

    CPT-81413-GENOMIC-PANEL-CARDIAC-ION-CHANNELOPATHIES

    CPT 81413: Cardiac Ion Channelopathy Targeted Gene Panel

    CPT-81414-CARDIAC-ION-CHANNELOPATHY-CNV-PANEL

    CPT 81414: Cardiac Ion Channelopathy Copy Number Variant Panel

    CPT-81416-FAMILIAL-EXOME-SEQUENCE-ANALYSIS

    CPT 81416: Relative Exome Sequence Analysis for Reference Exome

    CPT-81417-EXOME-SEQUENCE-REEVALUATION

    CPT 81417: Exome Reanalysis for New Clinical Information

    CPT-81418-PHARMACOGENOMIC-MULTIGENE-DRUG-METABOLISM-PANEL

    CPT 81418: Pharmacogenetic Multigene Panel Including CYP2C19 and CYP2D6

    CPT-81419-GENOMIC-SEQUENCE-PANEL-EPILEPSY

    CPT 81419: Genomic Sequence Analysis Panel for Epilepsy

    CPT-81420-NIPS-FETAL-ANEUPLOIDY-SEQUENCING-PANEL

    CPT 81420: Cell-Free Fetal DNA Panel for Chromosomes 13, 18, 21

    Showing 1–10 of 43

    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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    81417Exome; re-evaluation of previously obtained exome sequenceUsed when prior exome data are reanalyzed due to new gene knowledge or updated pipelines rather than a new sequencing run.
    81479Unlisted molecular pathology procedureUsed when a novel or nonstandard molecular procedure related to exome testing cannot be reported with existing codes.
    81228Cytogenomic constitutional (genome-wide) microarray analysisOften performed before or alongside exome sequencing to detect copy-number variants not reliably found by standard exome pipelines; complementary diagnostic test.