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Table 1 BRCA1 germline variants identified in Pakistani pancreatic cancer patients

From: Prevalence of BRCA1 and BRCA2 germline variants in an unselected pancreatic cancer patient cohort in Pakistan

Location

Coding (c.) DNA Sequencea

(amino acid change)

SNP ID

Effect

Prevalence, n (%)

Minor allele frequency (%)

Novel or previously reported

Cases N = 150

Controls N = 200

Cases

gnomAD, SAS

Variant of uncertain significance

       

Exon 11

c.878C > G (p.Thr293Ser)

rs747172803

Missense

1 (0.67)

1 (0.5)

0.333

0.013

ClinVar, LOVD

Benign/likely benign variants - coding

       

Exon 2

c.36A > G (p.Gln12Gln)

rs763230080

Silent

1 (0.67)

–

0.333

0.029

ClinVar, LOVD

Exon 8

c.536A > G (p.Tyr179Cys)

rs56187033

Missense

1 (0.67)

–

0.333

0.026

ClinVar, LOVD

Exon 11

c.823G > A (p.Gly275Ser)

rs8176153

Missense

2 (1.33)

–

0.667

0.459

ClinVar, LOVD

Exon 11

c.1067A > G (p.Gln356Arg)

rs1799950

Missense

1 (0.67)

–

0.333

1.316

ClinVar, LOVD

Exon 11

c.2077G > A (p.Asp693Asn)

rs4986850

Missense

10 (6.7)

–

3.333

3.536

ClinVar, LOVD

Exon 11

c.2082C > T (p.Ser694Ser)

rs1799949

Silent

34 (22.7)

–

11.33

50.4

ClinVar, LOVD

Exon 11

c.2311 T > C (p.Leu771Leu)

rs16940

Silent

34 (22.7)

–

11.33

50.3

ClinVar, LOVD

Exon 11

c.2521C > T (p.Arg841Trp)

rs1800709

Missense

1 (0.67)

–

0.333

0.183

ClinVar, LOVD

Exon 11

c.2612C > T (p.Pro871Leu)

rs799917

Missense

76 (50.7)

–

25.33

53.16

ClinVar, LOVD

Exon 11

c.2580A > G (p.Thr860Thr)

rs556684572

Silent

1 (0.67)

–

0.333

0.0098

ClinVar, LOVD

Exon 11

c.3113A > G (p.Glu1038Gly)

rs16941

Missense

2 (1.33)

–

0.667

50.35

ClinVar, LOVD

Exon 11

c.3119G > A (p.Ser1040Asn)

rs4986852

Missense

2 (1.33)

–

0.667

0.542

ClinVar, LOVD

Exon 13

c.4308 T > C (p.Ser1436Ser)

rs1060915

Silent

2 (1.33)

–

0.667

50.4

ClinVar, LOVD

Exon 16

c.4837A > G (p.Ser1613Gly)

rs1799966

Missense

8 (5.33)

–

2.667

50.4

ClinVar, LOVD

Exon 16

c.4883 T > C (p.Met1628Thr)

rs4986854

Missense

1 (0.67)

–

0.333

0.042

ClinVar, LOVD

Exon 16

c.4956G > A (p.Met1652Ile)

rs1799967

Missense

4 (2.67)

–

1.333

3.80

ClinVar, LOVD

Exon 20

c.5218G > A (p.Val1740Met)

–

Missense

1 (0.67)

0

0.333

–

Novel

Benign/likely benign variants - non-coding

       

Intron 7

c.442-34C > T

rs799923

Intronic

31 (20.7)

–

10.33

17.74

ClinVar, LOVD

Intron 8

c.547 + 36A > G

–

Intronic

1 (0.67)

–

0.333

–

Novel

Intron 13

c.4358-61C > G

–

Intronic

1 (0.67)

–

0.333

–

Novel

Intron 14

c.4484 + 14A > G

rs80358022

Intronic

1 (0.67)

–

0.333

0.0653

ClinVar, LOVD

Intron 14

c.4485-63C > G

rs273900734

Intronic

2 (1.33)

–

0.667

0

ClinVar, LOVD

Intron 15

c.4675 + 80C > T

–

Intronic

1 (0.67)

–

0.333

–

Novel

Intron 18

c.5152 + 41 T > C

–

Intronic

1 (0.67)

–

0.333

–

Novel

Intron 18

c.5152 + 66G > A

rs3092994

Intronic

2 (1.33)

–

0.667

0

ClinVar, LOVD

Intron 22

c.5406 + 33A > T

rs80358092

Intronic

1 (0.67)

–

0.333

0.066

ClinVar, LOVD

  1. gnomAD Genome Aggregation Database, LOVD Leiden Open Variant Database, SAS South Asians
  2. aNomenclature follows Human Genome Variation Society (HGVS) (http://www.hgvs.org). Numbering starts at the first A of the first coding ATG (located in exon 2) of NCBI GenBank Accession NM_007294.3
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Hereditary Cancer in Clinical Practice

ISSN: 1897-4287