The Non-Coding rs5945619 Variant at Xp11.22 and Its Putative Regulatory Effects on Nearby Genes in Ecuadorian Mestizo Women with Breast Cancer: A Case Series and In Silico Cis-eQTL Analysis

Breast cancer (BC) is a heterogeneous disease influenced by genetic and regulatory mechanisms. Despite this, X-linked non-coding variants remain underexplored, particularly in admixed Latin American populations. Therefore, this study aimed to characterize the non-coding variant rs5945619 at Xp11.22 in Ecuadorian mestizo women with BC and to assess its potential regulatory effects on nearby genes through in silico cis-eQTL analysis. A prospective observational case series was conducted in 21 Ecuadorian mestizo women with histologically confirmed BC. Tumor DNA was extracted and analyzed using the Illumina TruSight Cancer Sequencing Panel. The rs5945619 variant was identified from sequencing data and compared with reference allele frequencies from dbSNP, ALFA, and the 1000 Genomes Project. Regulatory potential was assessed using RegulomeDB v2.2, and tissue-specific cis-eQTL associations were explored using GTEx. All 21 patients carried the genetic variant rs5945619 in a heterozygous state. The mean age at diagnosis was 54.5 ± 12.2 years, and invasive breast carcinoma of no special type was the predominant histological subtype. The T-allele frequency in the study cohort was 0.50, whereas Latin American reference populations showed higher frequencies ranging from 0.69 to 0.83. RegulomeDB assigned rs5945619 a rank of 1f and a functional score of 0.22, supporting its regulatory potential. GTEx analysis identified tissue-specific cis-eQTL signals, including LINC01496 upregulation in testis, NUDT11 and LINC01496 downregulation in prostate, and modest GSPT2 downregulation in mammary tissue. This study provides the first characterization of rs5945619 in Ecuadorian mestizo women with BC and suggests its role as a potential X-linked regulatory variant, requiring further validation. Although universal heterozygosity was observed, the small sample size, tumor-only design, and absence of a healthy control cohort prevent any causal, risk-factor, or tumor-driven selection inference. The in silico evidence supports a tissue-dependent regulatory model involving LINC01496 and NUDT11, mainly in prostate/testis, and a modest GSPT2 signal in mammary tissue. Therefore, breast cancer-specific eQTL analyses, functional validation, and larger ancestry-informed case–control studies are required to determine the biological and clinical relevance of this locus.