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In the modern era, breast cancer (BC) is one of the most prevalent diseases affecting the lifespan of women. Single nucleotide polymorphism (SNP) elucidates an enormous proportion of the hazard in women with a solid family history. Different types of human disorders have been analyzed using Machine Learning methods to locate the vital SNP. The identification of an optimal feature set is the primary constraint in the existing methods owing to the ill effects of multidimensionality. Thus, a novel Bio-Inspired Ensemble Feature Selection (BIEFS) technique has been proposed in this paper to identify the most relevant SNP for accurate classification of BC. An initial feature subset is generated from each base feature selector such as Membership Weight Salp Swarm Algorithm (MWSSA), Crossover Horse Herd Optimization (CHHO), and Levy Mutation Manta-Ray Foraging Optimization (LMMRFO). Then the proposed BIEFS technique obtains the optimized weight of each feature subset through the mutation operator. Finally, the Self-Organizing Deep Auto-Encoder (SODAE) is employed for BC classification. A Gene Expression Omnibus (GEO) dataset is used to assess the proposed methodology. Simulation results validate that the proposed methodology attains a maximum accuracy of 98.75% as compared to the conventional techniques. [ABSTRACT FROM AUTHOR]