CPT 87490: Chlamydia trachomatis Direct Nucleic Acid Probe Test
CPT code 87490 denotes a laboratory diagnostic test using a direct nucleic acid probe to detect Chlamydia trachomatis, the pathogen responsible for a common sexually transmitted infection and certain eye infections. This molecular technique is an established diagnostic modality that supports timely identification and public health surveillance of chlamydial infection. Nationally, such tests influence clinical decision-making for treatment, contact tracing, and prevention of complications.
Key payers included in the analysis are Aetna, Blue Cross Blue Shield, Cigna Health, UnitedHealthcare, and Medicare. Readers will find a concise outline of the clinical context for the test, typical sites of service, and the service type. The publication also summarizes benchmarking and coverage considerations across major payers, highlights policy or coding updates when relevant, and lists associated billing elements for operational reference.
This report is intended to inform billing managers, lab administrators, and policy analysts about the role of CPT code 87490 in clinical workflows and payer interactions. Data not available in the input are explicitly omitted; the focus is on the code definition, clinical implications, payer coverage scope, and practical billing metadata.
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Billing Code Overview
CPT code 87490 describes a laboratory test in which a lab analyst performs a direct nucleic acid probe technique to detect Chlamydia trachomatis. The procedure identifies genetic material specific to the bacterium that causes common sexually transmitted infections and some ocular infections.
Service Type: Diagnostic laboratory testing — molecular direct probe
Typical Site of Service: Clinical laboratory or hospital laboratory
Clinical & Coding Specifications
Clinical Context
A sexually active 22-year-old female presents to an outpatient clinic with new-onset abnormal vaginal discharge and pelvic discomfort. The clinician performs a focused history and pelvic exam, collects an endocervical swab (or vaginal swab) specimen, and sends the sample to the laboratory for nucleic acid probe testing specifically for Chlamydia trachomatis. The laboratory analyst performs a direct nucleic acid probe assay, documents specimen acceptability, runs the assay according to manufacturer instructions, interprets results, and reports a positive or negative result to the ordering clinician. Positive results prompt partner notification and treatment per local public health guidance; negative results with persistent symptoms may lead to additional testing such as nucleic acid amplification tests (NAAT) or testing for other sexually transmitted infections.
Typical site of service: outpatient clinic or ambulatory care laboratory, sexually transmitted infection (STI) clinic, urgent care, or hospital outpatient laboratory.
Service type: laboratory diagnostic test — direct nucleic acid probe detection of Chlamydia trachomatis performed by a laboratory analyst.
Coding Specifications
| Modifier | Description | When to Use |
|---|---|---|
26 | Professional component | Use when reporting only the professional component of a test when the lab facility reports technical separately and a physician interprets results. |
59 | Distinct procedural service | Use when this test is performed on a separate anatomic site or on a separate and distinct encounter requiring separate reporting. |
62 | Two surgeons | Rarely used for lab tests; reported if two qualified practitioners share responsibility for the service in accordance with payer policy. |
78 | Unplanned return to the operating/procedure room | Not typically applicable to this lab test but included when a related procedure requires an immediate return. |
80 | Assistant at surgery | Not applicable to the laboratory test itself; used when an assistant surgeon is involved in a related procedure. |
90 | Reference (outside) laboratory | Use when the specimen is sent to an outside reference laboratory for testing and only reporting is performed by the ordering facility. |
TC | Technical component | Use when reporting only the technical component (laboratory performance of the assay) and the professional component is billed separately. |
QW | CLIA-waived test | Use when the performed test is CLIA-waived and the laboratory documents CLIA-waivered status for billing purposes. |
QX | CLIA moderate complexity, high complexity personnel | Use when the test requires personnel meeting CLIA moderate/high complexity personnel requirements and that is being reported per payer instructions. |
QY | CLIA waived under specific arrangement | Use when the test was performed under a CLIA waived category with a specific payer arrangement. |
AS | Physician assistant or other non-physician practitioner | Use when the service is performed or ordered by an advanced practice clinician and payer rules require this modifier. |
59 | Distinct procedural service | Use when multiple services on same date are distinct and need to be separately identified. |
52 | Reduced services | Use when the test was partially performed or limited in scope compared with the full procedure. |
90 | Reference lab outside laboratory | Use when the laboratory sends the specimen to an external reference lab for testing. |
| Taxonomy Code | Specialty | Notes |
|---|---|---|
| 207Q00000X | Obstetrics & Gynecology | Routine STI testing and specimen collection in female patients. |
| 207R00000X | Family Medicine | Primary care providers who collect specimens and manage STI testing. |
| 207L00000X | Internal Medicine | Primary care management and ordering of diagnostic STI tests. |
| 394NG0400X | Clinical Pathology (Laboratory) | Laboratory directors and analysts who perform and oversee the assay. |
| 363A00000X | Public Health & General Preventive Medicine | STI clinics and public health programs that order and follow-up on testing. |
Related Diagnoses
| ICD-10 Code | Description | Clinical Relevance |
|---|---|---|
A56.0 | Chlamydia trachomatis infection of lower genitourinary tract | Primary diagnosis indicating the presence of Chlamydia infection detected by this test. |
A56.2 | Chlamydia trachomatis infection of other specified sites | Used when Chlamydia infection is identified at sites such as the eye or rectum relevant to specimen source. |
N76.0 | Acute vaginitis | Symptom-driven diagnosis prompting testing for Chlamydia as part of vaginitis evaluation. |
N92.6 | Irregular menstruation, unspecified | Abnormal uterine bleeding can prompt STI testing including Chlamydia. |
H10.0 | Acute conjunctivitis | When conjunctival infection is suspected from Chlamydia trachomatis (tra choma or neonatal conjunctivitis), ocular swab testing may be indicated. |
R82.99 | Other abnormal findings in urine, unspecified | Abnormal urinalysis that leads to further testing for sexually transmitted pathogens using urine specimens. |
Z11.3 | Encounter for screening for infections with a predominantly sexual mode of transmission | Asymptomatic screening for Chlamydia where this test may be performed for routine screening. |
Related CPT Codes
| CPT Code | Description | Relationship to This Procedure |
|---|---|---|
87491 | Infectious agent detection by nucleic acid (DNA or RNA); Chlamydia trachomatis, amplified probe technique, direct probe with amplification | Alternative or complementary method: an amplified nucleic acid test that may be used instead of direct probe testing; typically more sensitive. |
87804 | Infectious agent antigen detection by enzyme immunoassay, direct probe or similar technique; Chlamydia trachomatis | Alternative laboratory method for antigen detection; may be used in different laboratory workflows. |
87624 | Infectious agent detection by nucleic acid (DNA or RNA); Chlamydia trachomatis, amplified probe technique, includes multiplex with Neisseria gonorrhoeae | Often ordered in combination to detect both Chlamydia and Gonorrhea from the same specimen; commonly used in STI screening. |
87070 | Culture, bacterial; any source except urine, blood or stool, aerobic with isolation and presumptive identification of isolates | May be ordered when additional bacterial culture is indicated, e.g., ocular infection or atypical presentations. |
81025 | Urinalysis, automated with microscopy | Often performed as part of STI evaluation when urinary symptoms are present; specimen source for some Chlamydia tests (urine NAATs). |