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The Taiwan Biobank (TWB) is a comprehensive nationwide genomic resource that captures the unique genetic diversity of the Taiwanese population. By reanalyzing whole-genome sequencing (WGS) data from 1,496 TWB participants, we generated high-confidence variant profiles and refined minor allele frequency (MAF) estimates. Each individual was found to carry an average of 6,870.7 globally novel variants, and 19.1% harbored at least one high-evidence human leukocyte antigen (HLA) risk allele relevant to pharmacogenomics. Notably, 1.67% of participants possessed medically actionable variants. Carrier rates for alpha thalassemia and spinal muscular atrophy were 5.12% and 1.6%, respectively. Leveraging precise MAF data and integrating it with real-world clinical cohorts, we developed a tiered diagnostic strategy for pediatric liver diseases that achieved diagnostic yields of 27.8% with targeted panels and up to 48.8% with whole-exome sequencing (WES). TWB’s WGS data also served as a robust population control in genetic studies. For example, in sensorineural hearing impairment (SNHI), the CRYL1 rs14236 variant was shown to amplify the phenotypic impact of the GJB2 p.V37I homozygotes (odds ratio = 5.2, p < 6.01×10⁻⁶). In a genome-wide association study (GWAS) of neovascular age-related macular degeneration (nAMD), we identified 16 risk loci, including both novel and established genes such as CFH and ARMS2/HTRA1, with three loci associated with suboptimal treatment responses. Collectively, these findings highlight the medical and scientific value of the TWB as a public dataset, enabling refined disease characterization, improved diagnostic strategies, and actionable insights for population health management. The integration of large-scale genomic data with clinical practice underscores the transformative potential of precision medicine for the Taiwanese population and sets a model for similar initiatives worldwide.