CPT 81425: Whole Genome Sequencing for Diagnostic Evaluation

Commercial payers pay $4542 on average nationally for this procedure.

CPT code 81425 describes a clinical laboratory service performing comprehensive whole genome sequencing to analyze the patient's entire genomic sequence for genetic variants that may explain an unexplained disorder or syndrome; this is a genomic sequencing diagnostic test typically performed as a clinical diagnostic laboratory service with the typical site of service being an outpatient or inpatient clinical laboratory affiliated with a hospital or specialized genetics testing center.

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National Reimbursement Benchmarks

National commercial reimbursement for CPT 81425 centers around the BUCA average commercial benchmark of $4,542.30, with payers showing meaningful variation around that midpoint. Blue Cross Blue Shield has one of the widest dispersions between the 25th and 75th percentiles (P75 $6,006.40 minus P25 $3,217.00 = $2,789.40), closely followed by Cigna (P75 $6,643.00 minus P25 $2,581.40 = $4,061.60) and UnitedHealth Group (P75 $5,031.20 minus P25 $2,113.10 = $2,918.10). Aetna displays a narrower interquartile spread (P75 $5,031.20 minus P25 $1,720.70 = $3,310.50) relative to Cigna and UnitedHealth Group but wider than some peers.

Dispersion highlights that Cigna exhibits the widest IQR at $4,061.60, signaling greater variability in mid‑range commercial payments, while Blue Cross Blue Shield and UnitedHealth Group also show substantial spreads of $2,789.40 and $2,918.10 respectively. BUCA’s average of $4,542.30 sits near payer medians overall, underscoring that commercial pricing for this code clusters around the mid single‑ to low five‑thousand dollar range despite notable inter‑payer variability.

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CPT 81425: Whole Genome Sequencing for Diagnostic Evaluation

Commercial payers pay $4542 on average nationally for this procedure.

Customize your policy alerts

Sign up for cpt 81425 policy alerts

Get alerted when payer policies referencing 81425 are released or updated.

Monitor payer policy activity

Receive email alerts as soon as relevant payer policies are published or updated.

National Reimbursement Benchmarks

National Payer Mean Reimbursement Rates

Clinical & Coding Specifications

Clinical Context

A pediatric patient is referred to a clinical genetics laboratory after presenting with multiple congenital anomalies, global developmental delay, and failure to thrive. Prior targeted genetic tests (chromosomal microarray and single-gene sequencing panels) were nondiagnostic. The clinician orders a comprehensive genome sequencing analysis to identify single nucleotide variants, small insertions/deletions, and structural variants across the entire genome. The typical workflow includes: sample collection (peripheral blood), accessioning, DNA extraction, library preparation, high-throughput sequencing, bioinformatic alignment and variant calling, multidisciplinary variant interpretation by a board-certified clinical molecular geneticist and laboratory director, and generation of a diagnostic report. Results may identify pathogenic or likely pathogenic variants explaining diagnoses such as Q90.9 (Down syndrome, if mosaic or atypical presentation), Q99.9 (chromosomal abnormality, unspecified), Q87.1 (congenital malformation syndromes), Q89.9 (congenital malformation, unspecified), or metabolic disorders like E88.9. Typical site of service is an outpatient clinical genetics or molecular diagnostics laboratory; sequencing may be ordered by specialists in genetics, pediatrics, neurology, or metabolic disease. The service type is comprehensive genome sequencing (diagnostic whole genome sequencing) performed for evaluation of unexplained genetic disorders.

Related CPT Codes

CPT Code	Description	Relationship to This Procedure
`81422`	Genomic sequencing procedure, advanced molecular analytics (subset)	May be used for targeted or smaller genomic panels when whole genome sequencing is not indicated; often performed before or instead of `81425`.
`81443`	Genomic sequencing procedure, interpretation and reporting of tumor or constitutional sequencing (larger panels)	Used for larger panel or exome-level analyses; may complement or be an alternative to whole genome sequencing.
`81426`	Genomic sequencing procedure, additional interpretation or specialized analysis	Billed for add-on or supplemental genomic analyses or expanded interpretation services that accompany primary genome sequencing.

Related Modifiers

8 rows

Modifier	Description	When to Use
26	Modifier 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…
90	Modifier ‑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…
59	Modifier 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…
62	Modifier 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…
80	CPT® 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…
22	Modifier –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…
52	Modifier ‑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…
53	Modifier 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…

Related Provider Taxonomies

8 rows

Taxonomy Code	Specialty	Notes
207SG0201X	Clinical Genetics (M.D.) Physician	A clinical geneticist demonstrates competence in providing comprehensive diagnostic, management and counseling services for genetic disorders.
207SG0202X	Clinical Biochemical Genetics Physician	A clinical biochemical geneticist demonstrates competence in performing and interpreting biochemical analyses relevant to the diagnosis and management…
207SG0205X	Ph.D. Medical Genetics Physician	A medical geneticist works in association with a medical specialist, is affiliated with a clinical genetics program and serves as a consultant to medi…
207SG0203X	Clinical Molecular Genetics Physician	A clinical molecular geneticist demonstrates competence in performing and interpreting molecular analyses relevant to the diagnosis and management of …
313M00000X	Nursing Facility/Intermediate Care Facility	An institution (or a distinct part of an institution) which- (1) is primarily engaged in providing to residents- (A) skilled nursing care and related …
323P00000X	Psychiatric Residential Treatment Facility	A residential treatment facility (RTF) is a facility or distinct part of a facility that provides to children and adolescents, a total, twenty-four ho…
246QH0000X	Hematology Specialist/Technologist	Technologists, Technicians & Other Technical Service Providers · Specialist/Technologist, Pathology
2279G1100X	General Care Registered Respiratory Therapist	This level of care includes diagnostics testing, therapeutics, monitoring, rehabilitation of patients with disorders of the cardiopulmonary system, as…

Related ICD-10-CM Codes

28 rows

ICD-10-CM Code	Description
D82.9	Immunodeficiency associated with major defect, unspecified
D84.9	Immunodeficiency, unspecified
E70.9	Disorder of aromatic amino-acid metabolism, unspecified
E88.9	Metabolic disorder, unspecified
F80.9	Developmental disorder of speech and language, unspecified
F82	Specific developmental disorder of motor function
G31.84	Mild cognitive impairment of uncertain or unknown etiology
G40.909	Epilepsy, unspecified, not intractable, without status epilepticus
H53.8	Other visual disturbances
H90.3	Sensorineural hearing loss, bilateral

Showing 1–10 of 28

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-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

Showing 1–10 of 43

References

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.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.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.

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Clinical & Coding Specifications

Clinical Context

Related CPT Codes

CPT Code	Description	Relationship to This Procedure
`81422`	Genomic sequencing procedure, advanced molecular analytics (subset)	May be used for targeted or smaller genomic panels when whole genome sequencing is not indicated; often performed before or instead of `81425`.
`81443`	Genomic sequencing procedure, interpretation and reporting of tumor or constitutional sequencing (larger panels)	Used for larger panel or exome-level analyses; may complement or be an alternative to whole genome sequencing.
`81426`	Genomic sequencing procedure, additional interpretation or specialized analysis	Billed for add-on or supplemental genomic analyses or expanded interpretation services that accompany primary genome sequencing.

Related Modifiers

8 rows

Modifier	Description	When to Use
26	Modifier 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…
90	Modifier ‑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…
59	Modifier 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…
62	Modifier 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…
80	CPT® 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…
22	Modifier –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…
52	Modifier ‑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…
53	Modifier 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…

Related Provider Taxonomies

8 rows

Taxonomy Code	Specialty	Notes
207SG0201X	Clinical Genetics (M.D.) Physician	A clinical geneticist demonstrates competence in providing comprehensive diagnostic, management and counseling services for genetic disorders.
207SG0202X	Clinical Biochemical Genetics Physician	A clinical biochemical geneticist demonstrates competence in performing and interpreting biochemical analyses relevant to the diagnosis and management…
207SG0205X	Ph.D. Medical Genetics Physician	A medical geneticist works in association with a medical specialist, is affiliated with a clinical genetics program and serves as a consultant to medi…
207SG0203X	Clinical Molecular Genetics Physician	A clinical molecular geneticist demonstrates competence in performing and interpreting molecular analyses relevant to the diagnosis and management of …
313M00000X	Nursing Facility/Intermediate Care Facility	An institution (or a distinct part of an institution) which- (1) is primarily engaged in providing to residents- (A) skilled nursing care and related …
323P00000X	Psychiatric Residential Treatment Facility	A residential treatment facility (RTF) is a facility or distinct part of a facility that provides to children and adolescents, a total, twenty-four ho…
246QH0000X	Hematology Specialist/Technologist	Technologists, Technicians & Other Technical Service Providers · Specialist/Technologist, Pathology
2279G1100X	General Care Registered Respiratory Therapist	This level of care includes diagnostics testing, therapeutics, monitoring, rehabilitation of patients with disorders of the cardiopulmonary system, as…

Related ICD-10-CM Codes

28 rows

ICD-10-CM Code	Description
D82.9	Immunodeficiency associated with major defect, unspecified
D84.9	Immunodeficiency, unspecified
E70.9	Disorder of aromatic amino-acid metabolism, unspecified
E88.9	Metabolic disorder, unspecified
F80.9	Developmental disorder of speech and language, unspecified
F82	Specific developmental disorder of motor function
G31.84	Mild cognitive impairment of uncertain or unknown etiology
G40.909	Epilepsy, unspecified, not intractable, without status epilepticus
H53.8	Other visual disturbances
H90.3	Sensorineural hearing loss, bilateral

Showing 1–10 of 28

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-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

Showing 1–10 of 43

References

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.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.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.

Published by

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