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CPT 81416: Familial Exome Sequence Analysis for Diagnostic Comparison
CPT code 81416 covers exome sequencing of a relative to create a reference exome that is compared with a patient’s exome to evaluate an unexplained disorder or syndrome. This familial comparative analysis is clinically important because it helps distinguish inherited benign variants from potentially pathogenic variants in the patient, improving diagnostic yield in complex genetic conditions. Nationally, use of familial exome analysis supports precision diagnosis in medical genetics and can affect downstream care planning and family counseling.
Key payers discussed in this analysis include Aetna, Blue Cross Blue Shield, Cigna Health, UnitedHealthcare, and Medicare. Readers will find a concise overview of the code’s clinical context, typical laboratory and site-of-service settings, and how the service fits within molecular diagnostic pathways. The publication summarizes payer coverage patterns, common billing and coding considerations, related molecular pathology CPT codes, and implications for genetic diagnostic workflows. It also outlines scenarios where familial exome comparison is clinically indicated and notes areas where policy language or coverage criteria may influence claim adjudication.
This summary provides clinicians, laboratory managers, and revenue cycle professionals with a national-level briefing on clinical purpose, payer scope, and operational context for CPT code 81416.
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Billing Code Overview
CPT code 81416 describes an exome gene sequence analysis performed in a relative of the patient to generate a reference exome for comparison with the patient’s exome. The procedure supports evaluation of an unexplained disorder or syndrome in the patient by identifying familial sequence variants that can clarify interpretation of the patient’s genomic findings.
Service type: Genetic testing — familial exome sequencing and comparative analysis
Typical site of service: Clinical molecular genetics laboratory
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.