dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs

Abstract

Whole exome sequencing has been increasingly used in human disease studies. Prioritization based on appropriate functional annotations has been used as an indispensable step to select candidate variants. Here we present the latest updates to dbNSFP (version 4.1), a database designed to facilitate this step by providing deleteriousness prediction and functional annotation for all potential nonsynonymous and splice-site SNVs (a total of 84,013,093) in the human genome. The current version compiled 36 deleteriousness prediction scores, including 12 transcript-specific scores, and other variant and gene-level functional annotations. The database is available at http://database.liulab.science/dbNSFP with a downloadable version and a web-service.

Keywords: Database; Deleteriousness prediction; Functional annotation; Nonsynonymous SNV; Whole exome sequencing.

Fig. 1

Violin plots of the dispersal statistic d for 12 transcript-specific deleteriousness prediction scores. d is capped at 10

Fig. 2

Pearson’s correlation coefficients of rank scores (upper triangle) and agreement ratio of binary predictions (lower triangle) between pairs of deleteriousness prediction scores or conservation scores

Fig. 3

UPGMA dendrogram of the deleteriousness prediction scores and conservation scores

Fig. 4

AUROC/VUROC scores for the top 5 deleterious prediction scores