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A first information report was registered at Police Station of Faisalabad District, Pakistan. A boy (7-8 years old) went to a nearby shop and went missing. He was last seen with the accused suspect on a motorcycle as reported by eye witnesses. His naked dead body was found from nearby sugarcane fields tied with his clothing.  Autopsy revealed three incised wounds on the neck. The post-mortem was done and anal swabs were used for DNA profiling. Post mortem medico legal examination indicated sexual abuse of the boy prior to being murdered. Forensic DNA analysis confirmed that the seminal material found on anal swabs of the victim belonged to the suspect. The same DNA profile was also found from the samples of nail scratch swab samples of the victim. The suspect was confirmed to be the perpetrator.

Background: The relationship testing through DNA profiling may undesirably be affected by the rare allele variants, tri-allelic pattern and null alleles. Therefore, it is vital to report such anomalies. We report a paternity testing in a sexual assault case studied at Punjab Forensic Science Agency, Lahore Pakistan showing a unique allele variant in mother and child. Methods: DNA was extracted from the buccal swabs of reference samples using organic extraction method and DNA profiling was done for 15 autosomal STRs and amelogenin using Identifiler Plus kit. Results: A novel out of marker range (OMR) allele variant between STR Loci D16S539 and D2S1338 was observed in the DNA profiles of victim (mother) as well as the child. At STR locus D2S1338 Twenty one different allele variant are listed at STRBase ranging from 11 to 28. The allele variant observed in this case study was appeared at less than marker range (< D2S1338) with a size of 297.50 bp. The novel variant OMR allele at D2S1338 was labeled as allele 13, when compared to the other allele in allelic ladder. Moreover, the PFSA DNA database was searched for this unique allelic variation and it was found that this was present in only two other samples of distinct cases. Conclusion: The overall frequency of this unique allele variant was 3 in 10,125 unrelated individuals with frequency of occurrence of 0.0296. According to our limited knowledge it is the first report of a novel OMR allele variant at D2S1338 in Pakistani Population.