Table 3.
Example default output of CAVA v.1.0
| 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 | . | . |
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