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

BMC Medical Genetics

Table 2 Number of variants obtained using different filters in subjects affected by splenic epidermoid cyst from Kosovo

Criteria for variants filtering	Kos-1	Kos-2	Kos-3	Kos-4
Total (Exonic, Splicing)	14817	14427	14783	14277
SNVs (NS, SC)	6701	6562	6734	6526
Not in dbSNP or 1000 Genomes (novel)	239	191	245	258
Up to 2% in 1000 Genomes	368	378	358	323
INDELs (FS, non-FS)	29	47	42	58
Not in dbSNP or 1000 Genomes (novel)	27	44	40	58
Up to 2% in 1000 Genomes	0	0	0	0

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 filter is based on the European allele frequencies data from 1000 Genomes database.

ISSN: 1471-2350