morrislab/vep-traitgym-mrna

Overview

The variant effect prediction task measures the pathogenicity of single nucleotide polymorpism (SNPs). This dataset is a reprocessing of the TraitGym dataset (https://huggingface.co/datasets/songlab/TraitGym), see original dataset for data generation process. We have filtered TraitGym to only include SNPs in mature mRNA UTR regions, and provide the mRNA transcript sequence context for the SNP using the principle isoform as determined by APPRIS.

This dataset is redistributed as part of mRNABench: https://github.com/morrislab/mRNABench

Data Format

Description of data columns:

• target: Whether the specified sequence contains a pathogenic mutation.
• cds: Binary track which reports position of first nucleotide in each codon in CDS.
• splice: Binary track which reports position of the 3' end of each exon, indicating splice sites.
• description: Description of the original mutation, in format chr{chr}:{position} {ref_base}:{alt_base}

Data Source

This dataset is generated using dataset collected by the Song lab as part of TraitGym, which is under an MIT license.

Please attribute:

TraitGym HuggingFace repository: : https://huggingface.co/datasets/songlab/TraitGym
TraitGym paper: https://www.biorxiv.org/content/10.1101/2025.02.11.637758v2
TraitGym GitHub: https://github.com/songlab-cal/TraitGym
Citation: Benegas, G., Eraslan, G., & Song, Y. S. (2025). Benchmarking DNA Sequence Models for Causal Regulatory Variant Prediction in Human Genetics. bioRxiv, 2025-02.