Congenital sensorineural hearing loss (SNHL) is recognized as a major public health burden. Mutations in the GJB2 gene are among the most frequent encountered etiological factors (approximately 50% of cases of autosomal recessive sensorineural non-syndromic hearing loss in the Caucasian population). Single nucleotide polymorphisms (SNPs) are important markers in studies that correlate the genotype with the phenotype. The main purpose of the study is to develop and validate a molecular-genetic screening algorithm based on the SNP rs80338939 for later use in laboratories in Romania and the Republic of Moldova. A prospective study was conducted on 50 randomly included subjects with profound congenital SNHL. The 35delG mutation was assessed by two methods: a reference method (University Medical Center Freiburg, Germany) and the method to validate: single nucleotide polymorphism (SNP) for the same mutation. We compared the results of the two methods to assess the specificity and sensitivity of the method used in the study. Results obtained indicate a sensitivity of 92% and 98% specificity for the studied method when compared with the reference method. The high sensitivity and specificity of the proposed method confirms that rs80338939 can be used as a biomarker in the assessment of the risk of autosomal recessive SNHL. In fact, we aim to optimize the technique to achieve 100% sensitivity and specificity. At the same time, we acknowledge that the screening of 35delG mutations does not replace the audiological screening tests, because the auditory function involves 1% of the human genes and mutations of any of these may lead to deafness.