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Table 4 Sherloc variant classification criteria of novel RECQL variants

From: Prevalence of RECQL germline variants in Pakistani early-onset and familial breast cancer patients

Variant

Evidence #

P/B

Points scorea

Evidence type

Category

c.225G > A (p.W75*)

EV0135

P

1

Clinical

Population - Frequency

EV0211

P

0

Clinical

Observation in Affecteds

EV0206

P

2

Clinical

Observation in Affecteds

EV0016

P

5

Functional

Variant Effect

Sum

8P

  

Sherloc score

Pathogenic

  

c.421A > T (p.I141F)

EV0101

P

0.5

Clinical

Population - Frequency

EV0211

P

0

Clinical

Observation in Affecteds

EV0172

P

1

Functional

Variant Effect

EV0121

P

1

Functional

Computational & Predictive

Sum

2.5P

  

Sherloc score

VUS

  

c.546C > T (p.S182S)

EV0101

P

0.5

Clinical

Population - Frequency

EV0211

P

0

Clinical

Observation in Affecteds

EV0193

P

1

Clinical

Observation in Affecteds

EV0103

B

2

Functional

Variant Effect

EV0191

B

1

Functional

Computational & Predictive

Sum

1.5P, 3B

  

Sherloc score

VUS

  

c.1425C > T (p.C475C)

EV0101

P

0.5

Clinical

Population - Frequency

EV0211

P

0

Clinical

Observation in Affecteds

EV0193

P

1

Clinical

Observation in Affecteds

EV0103

B

2

Functional

Variant Effect

EV0191

B

1

Functional

Computational & Predictive

Sum

1.5P, 3B

  

Sherloc score

VUS

  

c.868-2A > G

EV0096

B

5

Clinical

Population - Frequency

EV0053

B

2

Clinical

Observation in Unaffected

EV0037

B

1

Functional

Functional Experiment

EV0187

P

1

Functional

Computational & Predictive

Sum

1P, 8B

  

Sherloc score

Benign

  
  1. B Benign, EV Evidence, P Pathogenic, VUS Variant of unknown significance
  2. Pathogenicity and benign point scores are calculated separately
  3. aThe Sherloc point score thresholds for pathogenic and benign classifications are 5P and 5B, and for VUS <4P and < 3B
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Hereditary Cancer in Clinical Practice

ISSN: 1897-4287