Extended Data Fig. 5: Comparing RNA scores across timepoints.

a–c, Scores for n = 356 SNVs analyzed in exon 2 are plotted by transcript position. RNA scores are plotted for samples collected 6 days post-transfection (a) and 20 days post-transfection (b). Function scores are plotted for the same set of exon 2 variants (c). d, RNA scores correlate across timepoints (Pearson’s R = 0.86). Many variants with low RNA scores on day 6 have relatively higher RNA scores on day 20. (y = x plotted as a dashed line for reference.) e, The ΔRNA score for each SNV, defined as the day 20 RNA score minus the day 6 RNA score, is plotted for n = 184 LOF1, n = 81 LOF2, n = 118 intermediate and n = 1,226 neutral SNVs. Variants with day 6 RNA scores below the threshold of −3.0 are plotted separately for n = 10 LOF1, n = 5 LOF2 and n = 2 intermediate SNVs. (Boxplots: center line, median; box limits, upper and lower quartiles; whiskers, 1.5× interquartile range; all points shown.) f, SpliceAI component scores predict specific splice alterations, including acceptor loss, acceptor gain, donor loss and donor gain. Component SpliceAI scores are plotted against RNA scores for exonic SNVs.