Additional file 1 of Quantitative thresholds for variant enrichment in 13,845 cases: improving pathogenicity classification in genetic hearing loss

Additional file 1: Table S1. List of 115 SNVs and three CNVs in SNPscan assay. Table S2. 157 hearing loss related genes included in the CDGC-HL panel. Table S3. 9,050 variants included in this study. Table S4. Allele frequency thresholds for variants could reach p-value&lt;0.05 with different case sample size. Table S5. Variants in truth subset 1. Table S6. Variants in truth subset 2. Table S7. Variants in truth subset 3. Table S8. Evaluation metrics and positive likelihood ratio with different cutoffs in Truth Subset 1 and Truth Subset 3. Table S9. Summary of variants meeting the proposed PS4 thresholds. Table S10. The clinical and genetic findings of the 8 patients with upgraded P/LP variants. Table S11. CNVplex results of F3:II-1. Table S12. Correlation between PS4 and PM3 in the truth subset 3.附加文件1：表S1。SNPscan检测（SNPscan assay）中包含的115个单核苷酸变异（Single Nucleotide Variant, SNV）与3个拷贝数变异（Copy Number Variant, CNV）汇总列表。表S2：CDGC-HL检测panel中纳入的157个听力损失相关基因。表S3：本研究纳入的9050个变异位点。表S4：不同病例样本量下，变异位点达到p值<0.05的等位基因频率阈值。表S5：验证子集1中的变异位点。表S6：验证子集2中的变异位点。表S7：验证子集3中的变异位点。表S8：验证子集1与验证子集3中不同截断值下的评估指标与阳性似然比。表S9：符合所提出PS4阈值的变异位点汇总。表S10：8个携带升级为致病性/可能致病性（P/LP）变异患者的临床与遗传学发现。表S11：F3:II-1的CNVplex检测结果。表S12：验证子集3中PS4与PM3的相关性分析。