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Background  α-Thalassemia (α-thal) is a genetic disorder caused by the substitution of single amino acid or large deletions in the  HBA1  and/or  HBA2  genes.    Method  Using modern bioinformatics tools as a systematic  in-silico  approach to predict the deleterious SNPs in the  HBA1  gene and its significant pathogenic impact on the functions and structure of HBA1 protein was predicted.    Results and Discussion  A total of 389 SNPs in  HBA1  were retrieved from dbSNP database, which includes: 201 non-coding synonymous (nsSNPs), 43 human active SNPs, 16 intronic SNPs, 11 mRNA 3′ UTR SNPs, 9 coding synonymous SNPs, 9 5′ UTR SNPs and other types. Structural homology-based method (PolyPhen) and sequence homology-based tool (SIFT), SNPs&Go, PROVEAN and PANTHER revealed that 2.4% of the nsSNPs are pathogenic.    Conclusions  A total of 5 nsSNPs (G60V, K17M, K17T, L92F and W15R) were predicted to be responsible for the structural and functional modifications of HBA1 protein. It is evident from the deep comprehensive  in-silico  analysis that, two nsSNPs such as G60Vand W15R in  HBA1  are highly deleterious. These “2 pathogenic nsSNPs” can be considered for wet-lab confirmatory analysis.

In-Silico Computing of the Most Deleterious nsSNPs in HBA1 Gene