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    v1.0.30
    OpenPayerBilling CodesGenomic Sequencing Procedures and Other Molecular Multianalyte AssaysCPT cpt-81416-familial-exome-sequence-analysis
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    CPT 81416: Relative Exome Sequence Analysis for Reference Exome

    Commercial payers pay $10978 on average nationally for this procedure.

    CPT code 81416 describes laboratory analysis in which an exome from a relative is sequenced to create a reference exome that is compared with the patient’s exome to evaluate an unexplained genetic disorder or syndrome; this is a molecular diagnostic service typically performed as a laboratory-based exome sequencing analysis with the site of service most often being an outpatient clinical laboratory or specialized molecular genetics laboratory.

    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 reimbursement for CPT 81416 centers around BUCA’s mean commercial rate of $10,978.30, which serves as an indicative market average. Among large payers, Blue Cross Blue Shield’s mean is higher at $12,579 with a notable high outlier max of $73,877.10, while Cigna and Aetna cluster around $11,653.50 and $5,311 respectively; UnitedHealth Group’s mean is $9,567.80. These figures indicate a multi-thousand-dollar spread in commercial compensation for this genetic test across payer contracts.

    Dispersion measured by interquartile range (P75–P25) highlights variability: Blue Cross Blue Shield is tightest with a range of $5,018.35, UnitedHealth Group is relatively narrow at $6,960.00, and BUCA’s IQR is $6,488.00. Cigna and Aetna show wider spreads of $9,372.10 and $8,600.00 respectively, signaling greater inconsistency in negotiated commercial rates with those payers.

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    National Payer Mean Reimbursement Rates

    State Reimbursement Rates

    State: Alaska1 / 51

    Rate by payer

    Clinical & Coding Specifications

    Clinical Context

    A 6-year-old child presents to a pediatric genetics clinic with developmental delay, unexplained intellectual disability, and multiple congenital anomalies. The child underwent clinical exome sequencing which identified several variants of uncertain significance. To aid interpretation, the laboratory requests an exome sequence from a biologic parent to establish a reference (trio or duos) for comparison and to determine whether variants are de novo or inherited. The clinical workflow: the ordering clinician (clinical geneticist or pediatrician) obtains informed consent from the parent for genetic testing and documents the indication (evaluation of an unexplained disorder). The laboratory receives the parent sample, performs exome sequencing, and generates a reference exome. The lab bioinformatics team compares the proband’s exome to the relative’s exome to clarify variant inheritance and pathogenicity. Results are reported to the ordering clinician, who incorporates the interpretation into the patient’s diagnostic assessment and genetic counseling session.

    Related CPT Codes

    CPT CodeDescriptionRelationship to This Procedure
    81225CYP2C9 gene analysis, common variantsPharmacogenetic single-gene testing that may be ordered separately for drug metabolism evaluation; not a substitute for exome reference sequencing but may be co-ordered for medication management.

    Related Modifiers

    6 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…
    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…
    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…
    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
    207SG0202X
    207ZP0213X
    207Q00000X
    207R00000X
    207WX0110X
    146L00000X
    261QB0400X

    Related ICD-10-CM Codes

    32 rows

    ICD-10-CM CodeDescription
    C79.9Secondary malignant neoplasm of unspecified site
    D36.9Benign neoplasm, unspecified site
    D82.1Di George's syndrome
    E11.9Type 2 diabetes mellitus without complications
    E78.5Hyperlipidemia, unspecified
    F19.10Other psychoactive substance abuse, uncomplicated
    F82Specific developmental disorder of motor function
    F84.0Autistic disorder
    F84.5Asperger's syndrome
    G12.21Amyotrophic lateral sclerosis

    Showing 1–10 of 32

    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-81415-EXOME-SEQUENCE-ANALYSIS-UNEXPLAINED-DISORDER

    CPT 81415: Exome Sequence Analysis for Unexplained Disorder

    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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    Trek Health powers OpenPayer with a leading commercial payer intelligence platform, seamlessly converting fragmented payer data into actionable insights for provider organizations.

    Trek Health ingests and normalizes Transparency in Coverage data and payer policy updates to give provider organizations a clear view of how commercial reimbursement behaves across markets, payers, and services. Our platform transforms raw payer disclosures into structured intelligence that supports contract evaluation, payer negotiations, and service line strategy. By combining market benchmarks with ongoing policy visibility, Trek helps teams identify variability, risk, and opportunity in commercial reimbursement. The result is faster insight, stronger negotiating positions, and more informed financial decisions.

    81226
    CYP2D6 gene analysis, common variants
    Another pharmacogenetic single-gene test that can complement exome findings when drug response is a clinical concern; may be billed alongside targeted pharmacogenetic tests.
    81227CYP3A4 gene analysis, common variantsTargeted gene analysis for drug metabolism; can be performed in parallel if medication pharmacogenomics is relevant to the patient.
    81479Unlisted molecular pathology procedureUsed when a specific molecular procedure or analysis related to exome comparison is not described by an existing CPT; submit supporting documentation.
    81291NRAS gene analysis, variantsSingle-gene variant analysis used in oncology contexts; included as an example of targeted molecular testing that may be performed in related workflows when specific genes are implicated.