Table 1 Routine variant filtering criteria
From: Using multi-scale genomics to associate poorly annotated genes with rare diseases
Autosomal and X-linked recessive mode | Autosomal and X-linked dominant mode | |
|---|---|---|
Filtering criteria | Filtering criteria | |
1. Variant frequency | ||
gnomAD [42] | <= 0.02 | < 0.001 |
AF_popmax [42] | <= 0.02 | < 0.001 |
In-house exome database | <= 0.02 | < 0.001 |
2. Splicing and synonymous variants | ||
dbscSNV_RF_SCORE and dbscSNV_ADA_SCORE [43] | dbscSNV_RF_SCORE >= 0.5 or dbscSNV_ADA_SCORE >= 0.5 or SpliceAI >= 0.5 | dbscSNV_RF_SCORE >= 0.5 or dbscSNV_ADA_SCORE >= 0.5 or SpliceAI >= 0.5 |
SpliceAI [44] | ||
3. Nonsynonymous variants | ||
Polyphen2_HDIV_score [5] | Polyphen2_HDIV_score >= 0.5 or REVEL score >= 0.5 or SIFT score <= 0.5 | Polyphen2_HDIV_score >= 0.5 or REVEL score >= 0.5 or SIFT score <= 0.5 |
REVEL score [6] | ||
SIFT score [45] | ||