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. 2022 Mar 29;13:1655. doi: 10.1038/s41467-022-29271-y

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 6 — a, b The percentage of Authentic-Modified (AM) cryptic-donors correctly predicted, and decoy-donors incorrectly predicted at different cut-offs for (a) event rank in 40K-RNA and (b) SpliceAI (SAI) Δ score (donor_VAR -donor_REF). a The dotted line denotes cryptic- and decoy-donors predicted using a cut-off of events ranked 4 or less. 87% of cryptic-donors activated by AM-variants are among the top 4 events present in 40K-RNA within 250 nt of the annotated-donor, with 95% of decoy-donors not in the top 4 events. b While SpliceAI (SAI) outperforms other algorithms using a cut-off of Δ scores 0.1 and above (see supplementary Fig. 6a), it predicts only 75% of cryptic-donors (SAI Δ ≥ 0.1). SAI accurately excludes 99% of decoy-donors. c (top) Venn diagram showing the overlap of cryptic-donors with those predicted by SAI or our 40K-RNA method, among the entire pool of decoy-donors. (bottom) magnification of internal Venn. d Cryptic-donors activated by CM- and AM/CM-variants. (top) New GT/C (Light grey) denotes variants creating a GT or GC essential splice-site motif (40K-RNA is inherently unsuitable for these variants). Existing GT/C (blue) denotes variants that modify a decoy-donor with a pre-existing GC or GT essential splice-site. (bottom) For 40K-RNA, the orange segment denotes cryptic-donors in the top 4 events, yellow segment denotes where the cryptic-donor is present in 40k-RNA but is not in the top 4 events, and grey denotes cryptic-donors absent from 40K-RNA.