Table 1 List of structural variants identified by GRIDSS and filtered-in using our custom pipeline.

From: Optimizing GRIDSS for clinical use: A targeted NGS filtering strategy for germline structural variant detection

Patient ID

Gene

NCBI RefSeq

Predicted breakpoint(s)a

Sequencing instrument

Variant type (Length)

Variant location

HGVS coding DNA variant nomenclature (Traditional variant nomenclature)c

HGVS RNA variant nomenclatureb

HGVS protein variant nomenclatureb

Two-breakend structural variants

1

ATM

NM_000051.4

11:108190859-108190860

NextSeq

Duplication (34 bp)

Intron 44

c.6452+76_6452+109dup

r.(=)

p.(=)

2

BARD1

NM_000465.4

2:215609517-215609831

NextSeq

Deletion (313 bp)

Exon 9

c.1865_1903+274del

r.[1678_1903del, 1811_1903del]

p.[Met560Glyfs*2, Val604_Trp635delinsGly]

3

EPCAM

NM_002354.3

2:47596709-47601826

NextSeq

Deletion (5116 bp)

Exon 1

c.68_426-546del

r.?

p.?

4

EPCAM

NM_002354.3

2:47602010-47602368

HiSeq

Deletion (357 bp)

Intron 3

c.426-362_426-6del

r.?

p.?

5

MSH6

NM_000179.3

2:48033622-48033623

HiSeq

Duplication (29 bp)

Exon 9

c.3834_3862dup

 

p.(Lys1288Thrfs*49)

6

MSH6

NM_000179.3

2:48033711-48033768

NextSeq

Duplication (58 bp)

Exon 9

c.3922_3979dup

 

p.(Asn1327Thrfs*11)

7

MSH6

NM_000179.3

2:48033891-48033892

HiSeq

Duplication (30 bp)

Intron 9

c.4002-53_4002-24dup

r.(=)

p.(=)

8

PALB2

NM_024675.4

16:23646978-23647130

NextSeq

Duplication (153 bp)

Exon 4

c.739_891dup

 

p.(Thr247_Thr297dup)

One-breakend structural variants

9

APC

NM_000038.6

5:112174697

HiSeq

LINE1 insertion (L1Ta1d, 6057 bp)

Exon 16

NM_000038.6: c.3410_3411ins[PQ998981.1:g.1_6057] (c.3410_3411insLINE)

 

p.(Asp1137delinsGluArgArg*)

10

ATM

NM_000051.4

11:108106407

NextSeq

Alu insertion (AluYa5, 282 bp)

Exon 5

NM_000051.4: c.342_343ins[PX241358.1:g.1_282] (c.342_343insAlu)

 

p.(Leu115Glyfs*40)

11

BRCA2

NM_000059.4

13:32893302

NextSeq

Alu insertion (AluYa5, 280 bp)

Exon 3

NM_000059.4: c.156_157ins[PX241359.1:g.1_280] (c.156_157insAlu)

 

p.(Lys53Alafs*9)

12

BRCA2

NM_000059.4

13:32910689

NextSeq

Alu insertion (AluYb8, 284 bp)

Exon 11

NM_000059.4: c.2197_2198ins[PX241360.1:g.1_284] (c.2197_2198insAlu)

 

p.(Val733Glyfs*32)

13

PALB2

NM_024675.4

16:23614840

HiSeq

Alu insertion (AluYb8, 290 bp)

Exon 13

NM_024675.4: c.3501_3502ins[PX241361.1:g.1_290] (c.3501_3502insAlu)

 

p.(Asp1168Trpfs*32)

  1. aBreakpoint(s) predicted by GRIDSS algorithm.
  2. bWhen mRNA analysis was performed, HGVS RNA nomenclature reflects the observed transcript change. For variants without RNA analysis and no change expected, r.(=) and p.(=) are used, as recommended by HGVS.
  3. cTraditional variant nomenclature also used for Mobile Element Insertions.
  4. bp base pairs, LINE long interspersed nuclear element, LRS long-read sequencing, UTR untranslated region.
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