Annotated BED files of SNVs in Coding DNA Sequences (CDS) generated with VEP

These BED files represent Single Nucleotide Variants (SNVs) located in Coding DNA Sequences (CDS) of the human genome. The variants were extracted from public VCF files and annotated using the Variant Effect Predictor (VEP), based on canonical transcripts. Only variants mapped to CDS regions were retained, following MANE Select guidelines. These datasets were generated as part of a broader study investigating the mutational landscape of the human genome and the co-occurrence of variants with different evolutionary origins and functional consequences.

Each file contains a specific class of variants, as described below:

SNPs_CDS.bed.gz Biallelic polymorphic SNVs with allele frequency (AF) ≥ 1% in at least two of the seven global superpopulations from the Human Genome Diversity Project (HGDP).

rares_CDS.bed.gz Biallelic rare SNVs with AF < 1% across all seven HGDP superpopulations.

patho_CDS.bed.gz Pathogenic variants curated by ClinVar and associated with high-penetrance genetic diseases.

benign_CDS.bed.gz Benign variants curated by ClinVar, with no established association with disease.

cosmic_CDS.bed.gz Somatic SNVs derived from the COSMIC database, associated with tumor samples and cancer-related mutations.

These annotated datasets aim to support further genomic research and replication of our study findings.