Skip to main content

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