Table 1 Workflow of filtering the pathogentic variant
From: A de novo SCN8A heterozygous mutation in a child with epileptic encephalopathy: a case report
Variants No. | Note | |
|---|---|---|
GATK Haplotype (Total variants from a trio targeted-exome sequencing) | 20,076 | total variants from a parent-proband trio targeted sequencing |
1st round of Filtering criteria | variants were excluded using a hierachy of levels of filtering criteria | |
proband wild-type | 5971 | exclude variants only in the parants but not in the proband |
intron> 30 bp | 2490 | |
AF < 0.2 or AD< 4 or MQ < 35 | 1124 | |
SSR > =7 & AF < 0.3 indel | 1178 | |
indel> 50 bp | 4 | |
After 1st round of filtering | ||
Variants No. in the proband | 9309 | a five-tier system of classification for variants (ACMG guidelines, 2015) |
Benign | 8775 | |
Likely benign | 158 | |
Uncertain significance | 346 | |
Likely pathogenic | 23 | |
Pathogenic | 7 | |
2rd round of filtering criteria | ||
Pathogenic/Likly Pathogenic/Uncertain significance & OMIM | 368 | overlap these 3 types of variants with OMIM |
segregation analysis | 20 | a specific variant in the target gene is observed to segregate with a phenotype or disease |
variants which are associated with patient’s clinical phenotype | 1 | SCN8A:c.3953(exon22)A > G, p.Asn1318Ser, AF = 70/174 = 0.4 |
AF: allele frequency | ||
AD: allele depth | ||
MQ: Mapping quality | ||