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Table 3 Example default output of CAVA v.1.0

From: CSN and CAVA: variant annotation tools for rapid, robust next-generation sequencing analysis in the clinical setting

C
h
r
Pos Ref Alt Qual Filter Type ENST Gene TRINFO Loc CSN Class SO Impact Alt ann Alt class Alt SO
1 12009955 C T 200 PASS Substitution ENST00000196061 PLOD1 +/40.8 kb/19/2.9 kb Ex3 c.294C>T_p.= SY Synonymous_variant 3 . . .
1 12919891 G T 200 PASS Substitution ENST00000240189 PRAMEF2 +/4.8 kb/4/1.6 kb Ex3 c.631G>T_p.Glu211X SG Stop_gained 1 . . .
1 14106394 A ACTC 200 PASS Insertion ENST00000235372 PRDM2 +/120.2 kb/10/7.9 kb Ex8 c.2107_2109dupCCT_p.Pro703dup IF Inframe_insertion 2 c.2104_2105insCTC_p.Pro703dup . .
1 15789297 A C 200 PASS Substitution ENST00000359621 CELA2A +/15.4 kb/8/0.9 kb Ex4 c.297A>C_p.= SY Synonymous_variant 3 . . .
1 15812432 A G 200 PASS Substitution ENST00000375910 CELA2B +/15.3 kb/8/0.9 kb Ex6 c.530A>G_p.Gln177Arg NSY Missense_variant 2 . . .
1 16727305 G GCTT 200 PASS Insertion ENST00000335496 SPATA21 -/38.8 kb/13/2.0 kb Ex11 c.1081_1083dupAAG_p.Lys361dup IF Inframe_insertion 2 c.1078_1079insAGA_p.Lys361dup . .
1 22310824 T C 200 PASS Substitution ENST00000337107 CELA3B +/12.3 kb/8/0.9 kb Ex6 c.642 T>C_p.= EE Aplice_region_variant|synonymous_variant 2 . . .
1 31905889 A ACAG 200 PASS Insertion ENST00000373710 SERINC2 +/25.1 kb/11/2.1 kb Ex10 c.1129_1131dupCAG_p.Gln377dup IF Inframe_insertion 2 c.1116_1117insCAG_p.Gln377dup . .
1 36937059 A G 200 PASS Substitution ENST00000373103 CSF3R -/17.2 kb/17/3.5 kb Ex10 c.1260 T>C_p.= SY Synonymous_variant 3 . . .
1 38023316 C T 200 PASS Substitution ENST00000296218 DNALI1 +/9.9 kb/6/2.6 kb Ex2 c.260C>T_p.Ala87Val NSY Missense_variant 2 . . .
1 43771016 TA T 200 PASS Deletion ENST00000372476 TIE1 +/22.1 kb/23/3.9 kb In3/4 c.484 + 5delA SS5 Splice_donor_5th_base_variant 2 c.484 + 3delA . .
1 54605319 G GC 200 PASS Insertion ENST00000371330 CDCP2 -/14.8 kb/4/2.7 kb Ex4 c.1223_1224insG FS Frameshift_variant 1 . . .
1 55251689 T C 200 PASS Substitution ENST00000371276 TTC22 -/21.6 kb/7/3.3 kb Ex5 c.987A>G_p.= SY Synonymous_variant 3 . . .
1 55603581 T TA 200 PASS Insertion ENST00000294383 USP24 -/149.0 kb/68/10.8 kb In26/27 c.2929-5dupT SS Intron_variant|splice_region_variant 3 c.2929-9_2929-8insT INT intron_variant
1 60503762 T C 200 PASS Substitution ENST00000371201 C1orf87 -/83.4 kb/12/2.0 kb Ex6 c.765A>G_p.= SY Synonymous_variant 3 . . .
1 62232031 C T 200 PASS Substitution ENST00000371158 INADL +/421.4 kb/43/8.5 kb Ex4 c.270C>T_p.= SY Synonymous_variant 3 . . .
1 67155862 TCTC T 200 PASS Deletion ENST00000371037 SGIP1 +/210.8 kb/25/4.6 kb In16/17 c.1444-8_1444-6delCCT SS Intron_variant|splice_region_variant 3 c.1444-10_1444-8delCTC . .
  1. Chr chromosome, Pos position, Ref reference alllele, Alt alternative allele, Qual quality score, TRINFO transcript information, Loc location in transcript, Alt ann alternative annotation, Alt class alternative class, Alt SO alternative SO term