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Zero-shot SpliceVarDB intronic SNVs classification (Evo 2 paper, Supplementary Data 1)

Zero-shot classification of splice-altering versus other variants in the SpliceVarDB intronic SNVs stratum, AUROC and AUPRC.

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Stable ID: gfm-guides-20261014-evo2-brixi2026-protocol-splicevardb-intronic-snv

areas
dna-genomes
contexts
research
protocol
Score each variant zero-shot (for Evo 2, the log-likelihood of the variant sequence minus that of the reference over an 8,192-bp genomic window around the variant) and compute AUROC and AUPRC for splice-altering versus other variants in the stratum Data 'SpliceVarDB', Genomic_Feature 'Intronic', Variant_Type 'SNV'.
version
As published, Nature 652 (2026), Supplementary Data 1
source locator
Supplementary Data 1 rows with Data 'SpliceVarDB', Genomic_Feature 'Intronic', Variant_Type 'SNV', Sub_category ''; SI A.3.12 and A.3.14 (pages 13 and 14); Fig. 3d
limitations
Positives: 2567 splice-altering; negatives: 1141 other; total 3708 variants (Supplementary Data 1).; No split: every model scores the same variants zero-shot (SI A.3.12: 'For each benchmark, we score the same variants with all models').; Supervised comparators (AlphaMissense, CADD, SpliceAI, Pangolin) may have been trained on overlapping variants; training overlap is not reported.; No uncertainty is reported.
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