The chromosomal region around 14q22-q23 containing bmp4 gene is extensively studied by genotyping to give evidence of linkage and one of the most functional single-nucleotide polymorphisms (SNPs) of BMP4 gene, rs17563, is currently a research focus which is a promising in NSCL/P development. Aim: This study was done to identify Single nucleotide polymorphism that confirmed change from T to C at 538 nucleotide position (538T/C). Method: The sequencing pattern of the base pairs at BMP4 538T/C position to find out subsequent polymorphism, resulting in an amino acid change of Val=Ala (V152A) in the polypeptide chain in cleft lip and palate patients using the most common bioinformatics analyses, Multiple Sequence Alignment (MSA) that involve comparing homologous sequences and then further alignment by Clustal Omega, a progressive method MSA. Results: Our results showed that 71.4% of the samples represented the nucleotide as C and 28.5% showed presence of nucleotide T at SNP point mutation site. Conclusion: Sequencing in our present study confirms the previous results of our findings of PCR restriction fragment length polymorphism on NSCLP in an Indian population that C genotype has more risk for NSCLP.