Table 1 Observed number of variant calls, VAPs and deletions with two different cohort allele frequency thresholds (10% and 0.5%) in our cohort of 41,755 exome samples
From: Systematic analysis of paralogous regions in 41,755 exomes uncovers clinically relevant variation
Variant type | Due to ectopic gene conversion | Within or outside an OMIM disease gene | Transcript consequence | VAF threshold | Number of variants/VAPs |
|---|---|---|---|---|---|
deletion | NA | Within | NA | 0.10 | 6250 |
deletion | NA | Outside | NA | 0.10 | 14,182 |
SNV/Indel | Yes | Within | LoF | 0.10 | 1043 |
SNV/Indel | Yes | Within | Miss | 0.10 | 4507 |
SNV/Indel | Yes | Within | Rest | 0.10 | 56,279 |
SNV/Indel | Yes | Outside | LoF | 0.10 | 341 |
SNV/Indel | Yes | Outside | Miss | 0.10 | 10,970 |
SNV/Indel | Yes | Outside | Rest | 0.10 | 264,944 |
SNV/Indel | No | Within | LoF | 0.10 | 13,875 |
SNV/Indel | No | Within | Miss | 0.10 | 142,324 |
SNV/Indel | No | Within | Rest | 0.10 | 524,376 |
SNV/Indel | No | Outside | LoF | 0.10 | 53,908 |
SNV/Indel | No | Outside | Miss | 0.10 | 514,659 |
SNV/Indel | No | Outside | Rest | 0.10 | 3,347,319 |
deletion | NA | Within | NA | 0.005 | 1182 |
deletion | NA | Outside | NA | 0.005 | 3885 |
SNV/Indel | Yes | Within | LoF | 0.005 | 181 |
SNV/Indel | Yes | Within | Miss | 0.005 | 1279 |
SNV/Indel | Yes | Within | Rest | 0.005 | 22,831 |
SNV/Indel | Yes | Outside | LoF | 0.005 | 341 |
SNV/Indel | Yes | Outside | Miss | 0.005 | 480 |
SNV/Indel | Yes | Outside | Rest | 0.005 | 60,298 |
SNV/Indel | No | Within | LoF | 0.005 | 2000 |
SNV/Indel | No | Within | Miss | 0.005 | 20,827 |
SNV/Indel | No | Within | Rest | 0.005 | 79,037 |
SNV/Indel | No | Outside | LoF | 0.005 | 8760 |
SNV/Indel | No | Outside | Miss | 0.005 | 79,962 |
SNV/Indel | No | Outside | Rest | 0.005 | 482,720 |
