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TAVR has emerged as a standard approach for treating severe aortic stenosis patients. However, it is associated with several clinical complications, including subclinical leaflet thrombosis characterized by Hypoattenuated Leaflet Thickening (HALT). A rigorous analysis of TAVR device thrombogenicity considering anatomical variations is essential for estimating this risk. Clinicians use the Sinotubular Junction (STJ) diameter for TAVR sizing, but there is a paucity of research on its influence on TAVR devices thrombogenicity. A Medtronic Evolut® TAVR device was deployed in three patient models with varying STJ diameters (26, 30, and 34 mm) to evaluate its impact on post-deployment hemodynamics and thrombogenicity, employing a novel computational framework combining prosthesis deployment and fluid-structure interaction analysis. The 30 mm STJ patient case exhibited the best hemodynamic performance: 5.94 mmHg mean transvalvular pressure gradient (TPG), 2.64 cm2 mean geometric orifice area (GOA), and the lowest mean residence time (TR)—indicating a reduced thrombogenic risk; 26 mm STJ exhibited a 10 % reduction in GOA and a 35% increase in mean TPG compared to the 30 mm STJ; 34 mm STJ depicted hemodynamics comparable to the 30 mm STJ, but with a 6% increase in TR and elevated platelet stress accumulation. A smaller STJ size impairs adequate expansion of the TAVR stent, which may lead to suboptimal hemodynamic performance. Conversely, a larger STJ size marginally enhances the hemodynamic performance but increases the risk of TAVR leaflet thrombosis. Such analysis can aid pre-procedural planning and minimize the risk of TAVR leaflet thrombosis. [ABSTRACT FROM AUTHOR]