The DNA-based method is used widely for HLA genotyping in routine work, but some allele may be dropout in the genotyping procedure. Here, we reported a case with HLA-A allele dropout in the Sanger PCR-SBT test. The initial PCR-SBT method with a commercial agent kit was not characterized, and the result of Luminex technology indicated the dropout as a HLA-A*02 allele. Subsequently, the sequences of exons 2–4 were fully matched with the A*02:07 and A*11:01:01 by allele group-specific primer amplification PCR-SBT. On further analysis, a novel allele A*02:07:07 was identified, which has one nucleotide difference from A*02:07:01 at position 6 C>G of exon 1. According to the sequencing for 5′-UTR to 3′-UTR, the novel single nucleotide polymorphism of exon 1 was contributed to HLA-A locus allele dropout in the sample. Our results indicated multiplatform analysis is necessary when a conclusive HLA type cannot be determined by a single methodology.