Genomic testing, variant interpretation, and counselling — formative SAQs

SAQ 1 (10 marks)

A four-year-old boy is referred for global developmental delay, mild dysmorphic features, and a paternal family history of learning difficulty. His chromosomal microarray returned normal. The paediatrician has now ordered trio exome sequencing. The parents ask what this test involves and what it might find. [2] [9]

a) Explain why a normal chromosomal microarray does not exclude a genetic diagnosis, and justify the escalation to exome sequencing. (3 marks) [2] [9]

b) Describe the ACMG/AMP five-tier variant classification framework, naming each tier and giving the approximate probability range for a variant of uncertain significance. (3 marks) [1]

c) Outline the domains you would cover in the pre-test counselling conversation, including the option of secondary findings and the management of a potential VUS. (2 marks) [5] [9]

d) Explain why trio sequencing (proband plus both parents) is preferred over proband-only sequencing, naming two advantages. (2 marks) [9]

SAQ 2 (10 marks)

A six-year-old girl with intellectual disability and seizures undergoes trio genome sequencing. The laboratory report returns a likely pathogenic variant in a gene associated with a neurodevelopmental disorder and, separately, a pathogenic variant in a cardiac arrhythmia gene on the ACMG SF v3.0 list that is unrelated to her presenting phenotype. The family consented to secondary findings at the pre-test visit. [1] [5]

a) Explain the difference between a likely pathogenic variant and a variant of uncertain significance, and state how each should be managed clinically. (3 marks) [1]

b) Define a secondary finding, explain the ACMG SF v3.0 list, and describe the management steps that follow the detection of this cardiac arrhythmia variant. (3 marks) [5]

c) Outline the cascade-testing obligation for this family, including who should be tested and why. (2 marks) [9]

d) Describe the plan for the non-diagnostic aspects of this result, including the role of periodic re-analysis. (2 marks) [9]

Marking guide

SAQ 1. Chromosomal microarray detects copy-number variants (deletions and duplications) at sub-microscopic resolution and is the first-tier test for unexplained developmental disability, but it does not detect single-nucleotide variants, repeat expansions (such as fragile X), balanced rearrangements (translocations, inversions), or epigenetic changes. A normal microarray has excluded pathogenic CNVs, not the broader universe of genetic disease, so escalation to exome sequencing is justified when the phenotype is consistent with a single-gene disorder. The ACMG/AMP five-tier framework classifies variants as pathogenic (greater than 99 percent probability), likely pathogenic (90 to 99 percent), VUS (5 to 90 percent), likely benign (1 to 5 percent), and benign (less than 1 percent), built on evidence codes for population frequency, computational prediction, functional impact, and segregation. Pre-test counselling covers the estimated diagnostic yield, the possibility of a VUS, the option of secondary findings (the ACMG SF v3.0 list of 73 medically actionable genes, opt-in), insurance and employment protections, and data-sharing consent. Trio sequencing is preferred because it identifies de novo variants (a powerful indicator when the phenotype fits) and filters the vast number of rare inherited variants, reducing VUS burden and increasing diagnostic yield. [1] [2]

SAQ 2. A likely pathogenic variant carries 90 to 99 percent probability of causing disease and is treated clinically as if pathogenic, driving surveillance, management, and family testing; a VUS carries 5 to 90 percent probability and should not drive clinical management alone — it should prompt segregation testing, functional studies where available, and periodic re-analysis. A secondary finding is a clinically actionable variant in a gene unrelated to the indication for testing, reported under the ACMG SF v3.0 list (a policy statement listing 73 medically actionable genes for which findings are offered when the family opts in). The cardiac arrhythmia variant triggers referral to a cardiologist, baseline cardiac assessment (ECG, echocardiography), disease-specific surveillance, and potentially prophylactic treatment. Cascade testing should include both parents (to confirm de novo versus inherited status and establish the inheritance pattern), siblings, and at-risk relatives on the relevant side of the family, coordinated through the genetics service. The non-diagnostic aspects — any VUS or unexplained findings — should be managed with segregation testing, functional studies where available, and a commitment to periodic re-analysis every 2 to 3 years as new genes are discovered and variant knowledge grows. [1] [5]