Clinical implementation of mutational analysis for NGS-based assays has largely been of a binary nature with pathogenic mutations being reported as either positive or negative. Actionability on the continuous output of variant allele frequency (VAF) has not been well characterized in the clinical setting, limiting its use. In this paper, analytical validity and the performance of the short variant VAF based on an NGS-based liquid biopsy assay, FoundationOne Liquid CDx (F1LCDx), was evaluated through assessment of precision, analytical accuracy, limit of blank (LoB), and limit of detection (LoD). Analytical validation of VAF values measured by F1LCDx supports that these values are accurate, precise, robust, and linear with the true VAF value. The association of allele frequency of clinically relevant short variants in circulating-free DNA (cfDNA) and the association with overall survival (OS) for patients using real-world data was also assessed. The results of the association analysis indicated that VAF of the predictive biomarker mutation negatively correlated with OS of NSCLC patients.