It is possible to estimate the prior probability of pathogenicity for germline disease gene variants based on bioinformatic prediction of variant effect/s. However, routinely used approaches have likely led to the underestimation and underreporting of variants located outside donor and acceptor splice site motifs that affect messenger RNA (mRNA) processing. This review presents information about hereditary cancer gene germline variants, outside native splice sites, with experimentally validated splicing effects. We list 95 exonic variants that impact splicing regulatory elements (SREs) in BRCA1, BRCA2, MLH1, MSH2, MSH6, and PMS2. We utilized a pre‐existing large‐scale BRCA1 functional data set to map functional SREs, and assess the relative performance of different tools to predict effects of 283 variants on such elements. We also describe rare examples of intronic variants that impact branchpoint (BP) sites and create pseudoexons. We discuss the challenges in predicting variant effect on BP site usage and pseudoexonization, and suggest strategies to improve the bioinformatic prioritization of such variants for experimental validation. Importantly, our review and analysis highlights the value of considering impact of variants outside donor and acceptor motifs on mRNA splicing and disease causation.

中文翻译：

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对剪接调控元件、分支点使用和伪外显子化的变异效应：以遗传性癌症基因为范例增强生物信息学预测的策略。

基于变异效应的生物信息学预测，可以估计种系疾病基因变异的致病性先验概率。然而，常规使用的方法可能导致低估和低估了位于供体和受体剪接位点之外的影响信使 RNA (mRNA) 处理的变异。本综述介绍了有关遗传性癌症基因种系变异的信息，这些变异位于天然剪接位点之外，具有经过实验验证的剪接效果。我们列出了 95 种影响BRCA1、BRCA2、MLH1、MSH2、MSH6和PMS2中剪接调控元件 (SRE) 的外显子变异. 我们利用预先存在的大规模 BRCA1 功能数据集来映射功能 SRE，并评估不同工具的相对性能以预测 283 种变体对此类元素的影响。我们还描述了影响分支点 (BP) 站点和创建假外显子的内含子变异的罕见示例。我们讨论了预测变异对 BP 位点使用和伪外显子化的影响的挑战，并提出了改进此类变异的生物信息学优先级以进行实验验证的策略。重要的是，我们的回顾和分析强调了考虑供体和受体基序之外的变异对 mRNA 剪接和疾病因果关系的影响的价值。