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Supplementary Figure S2. A. Proportion of VUS with different pathogenic probabilities estimated from a calibrated algorithm based on customized MAPP and Polyphen2 scores; B. Proportion of VUS per gene with different pathogenic probabilities; C. Distribution of probabilities of pathogenicity for all four MMR genes; D. MLH1; E. MSH2; F. MSH6; G. PMS2 genes.

S1. Variants of unknown significance detected in the MD Anderson cohort. S2. Clinical characteristics of the VUS carriers reported in Supplementary Table 1. Pathogenic mutations detected in the same patient carrying a VUS are presented in bold. S3. Clinical characteristics of carriers of variants reclassified as InSIGHT Class 1 and 5. These variants have been used for validation purposes. S4. Validation set of splicing variants obtained from the InSiGHT database that have been already reclassified as Class 1 and 5. S5. Classification at the RNA level using three bioinformatic in silico programs of all reported VUS. Results in gray indicate major alterations which are those that are predicted to destroy or create splicing sites or produce a SS score modification {greater than or equal to}20%; Predictions are interpreted as inconclusive when the same results are not obtained by all the programs used. S6. Detailed results of in silico RNA bioinformatic prediction tools for those variants classified as affecting Splicing Sites or Inconclusive by In silico prediction tools. Results in gray indicate major alterations. For splice site predictions, major alterations are those that are predicted to destroy or create splicing sites or produce a SS score modification {greater than or equal to}20%; Predictions are interpreted as inconclusive when the same results are not obtained by all the programs used. S7. Splicing validation set using three bioinformatic in silico programs of a set of splicing variants obtained from the InSIGHT database and that have been already re-classified as Class 1 and 5. Results in gray indicate major alterations, which are destroyed or created SS or score modifications {greater than or equal to}20%; Predictions are interpreted as inconclusive when only one program predict pathogenicity. S8. Detailed in silico RNA bioinformatic prediction results for splicing variants already reclassified as class 5 used for validation of in silico tools. Variants presented here were predicted to be Aberrant or Inconclusive based on our RNA in silico approach. Results in gray indicate major alterations. For splice site prediction, major alternations are destroyed or created SS or score modifications {greater than or equal to}20%; Predictions are interpreted as inconclusive when the same results are not obtained by all the programs used. S9. Classification at protein level of reported VUS using five bioinformatic in silico programs. Results in gray indicate major alterations. Predictions are interpreted as inconclusive when the same results are not obtained by all the programs used. S10. Detailed results of in silico analysis at protein level. S11. Summary of the clinical characteristics and mRNA and protein in silico predictions of the identified MMR VUS. Raw data concerning these analyses is detailed in Supplementary Tables 1-6. S12. Classification at the RNA level using three bioinformatic in silico programs of Identified Variants reclasified as InSIGHT Class 1 and 5 from the MD Anderson database. These variants have been used for validation purposes. Results in gray indicate major alterations, which are destroyed or created SS or score modifications {greater than or equal to}20%; Predictions are interpreted as inconclusive when only one program predict pathogenicity. S13. Detailed in silico RNA bioinformatic prediction results for variants reclassified as InSIGHT class 1 and 5 that obtained results of affecting splicing sites or Inconclusive. Results in gray indicate major alterations. For splice site prediction, major alternations are destroyed or created SS or score modifications {greater than or equal to}20%; Predictions are interpreted as inconclusive when the same results are not obtained by all the programs used. S14. Classification at protein level using five bioinformatic in silico programs of variants reclassified as InSIGHT Class 1 and 5. These variants were used for validation purposes. Results in gray indicate major alterations. Predictions are interpreted as inconclusive when the same results are not obtained by all the programs used. S15. Summary of the clinical characteristics and mRNA and protein in silico analyses of variants reclassified as InSIGHT Class 1 and 5. These variants were used for valiadation purposes. Information concerning these variants is detailed in supplementary Tables 8-11.

Background Although intensity-modulated radiation therapy (IMRT) is considered the standard of care for the treatment of squamous cell carcinoma of the anus (SCCA), few large series have reported oncologic outcomes and toxicities. In this retrospective report, we aim to describe outcomes and toxicities after IMRT-based chemoradiation (CRT) for the treatment of SCCA, evaluate the impact of dose escalation (>54 Gy), and compare concurrent fluoropyrimidine in combination with either mitomycin or with cisplatin as chemosensitizers. Methods Patients treated at The University of Texas MD Anderson Cancer Center between January 1, 2003 and December 31, 2018 with IMRT-based CRT were included. Median time to locoregional recurrence, time to colostomy, and overall survival were estimated using the Kaplan–Meier method. Results A total of 428 patients were included; median follow-up was 4.4 years. Three hundred and thirty-four patients (78.0%) were treated with concurrent cisplatin and fluoropyrimidine, and 160 (37.4%) with >54 Gy. Two- and 5-year freedom from locoregional failure, freedom from colostomy failure, and overall survival were 86.5% and 81.2%, respectively, 90.0% and 88.3%, respectively, and 93.6% and 85.8%, respectively. Neither dose escalation nor mitomycin-based concurrent chemotherapy resulted in improved outcomes. Mitomycin-based concurrent chemotherapy was associated with in approximately 2.5 times increased grade 3 or greater acute toxicity. Radiation dose >54 Gy was associated with approximately 2.6 times increased Grade 3 or greater chronic toxicity. Conclusions Our results suggest IMRT-based CRT with concurrent fluoropyrimidine and cisplatin is a safe and feasible option for patient with SCCA and may cause less acute toxicity. The role for radiation dose escalation is unclear and requires further study.