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Table 1 Number of variants obtained using different filters in a family of splenic epidermoid cyst

From: Genome-wide linkage and exome analyses identify variants of HMCN1for splenic epidermoid cyst

Criteria for variants filtering AFFECTED NOT AFFECTED UNCONFIRMED*
III:2 IV:3 IV:4 II:2 III:1 II:1 II:3 II:5
Total (Exonic, Splicing) 22903 23110 22925 22686 22705 23389 22900 22748
SNVs (NS, SC) 10735 10836 10679 10576 10641 10939 10630 10576
Not in dbSNP or 1000 Genomes 630 625 606 606 576 687 648 664
Within linkage region         
Chr. 1: 181,329,185-211,652,186 bp 8 6 8 9 8 6 7 6
Chr. 14: 36,888,531-58,397,917 bp 5 4 2 2 3 3 4 2
Shared by all AFFECTED 2 (CNTN2 & DDHD1) 2 2 2 - - 1 (DDHD1) 1
INDELs (FS, non-FS) 218 222 224 232 231 226 232 235
Not in dbSNP or 1000 Genomes 23 25 26 23 19 31 32 25
Within linkage region         
Chr. 1: 181,329,185-211,652,186 0 0 0 0 0 1 0 0
Chr. 14: 36,888,531-58,397,917 0 0 0 0 0 0 0 0
Rare variants         
Total (NS, SC, FS, Non-FS) 352 360 350 335 337 352 336 367
Within linkage region         
Chr. 1: 181,329,185-211,652,186 3 5 5 6 4 5 8 11
Chr. 14: 36,888,531-58,397,917 0 0 0 0 0 0 0 0
Shared by all AFFECTED 1 (HMCN1) 1 1 1 - - - -
  1. Exonic and splicing site variants were filtered based on being single nucleotide variants (SNVs) including non-synonymous (NS) and stop codon (SC) variants, while insertion/deletion (INDELs) including frame-shift (FS) and non-frame-shift (non-FS) variants. Novel variants were those not reported in dbSNP database (dbSNP 137) and rare variants (up to 2%) filter is based on the Japanese allele frequencies data from 1000 Genomes database. *Those family members were set as UNCONFIRMED because their affection status was based on clinical examination of the spleen.