NeuroGenetics Curriculum·intermediate·30 min

CNV Interpretation

A clinical framework for classifying copy number variants — from detection technologies to the ACMG/ClinGen scoring system — with an emphasis on recurrent genomic disorders in neurogenetics.

Tags: Neurogenetics · Advanced

Learning Objectives

  1. 1.Define copy number variants and describe their detection by chromosomal microarray and genome sequencing
  2. 2.Apply the ACMG/ClinGen CNV interpretation framework to classify deletions and duplications
  3. 3.Evaluate the five major evidence categories used in CNV pathogenicity assessment
  4. 4.Recognize recurrent genomic disorders caused by CNVs in neurogenetic practice
  5. 5.Correctly communicate CNV findings and their clinical implications

01Copy Number Variants: Definition and Clinical Significance

Copy number variants (CNVs) are structural genomic variants in which a segment of DNA is present at a copy number that differs from the normal diploid state. CNVs range from kilobases to megabases in size and can involve deletions (loss) or duplications (gain). They are a major source of both normal human genomic variation and serious neurogenetic disease.

Key Points

  • CNV classification by size: chromosomal microarray typically detects CNVs ≥50–200 kb; WGS can detect CNVs as small as a few hundred base pairs
  • Population CNVs: many CNVs are common (>1% frequency) and benign; catalogued in the Database of Genomic Variants (DGV) and gnomAD-SV
  • Pathogenic CNVs: typically rare (<0.01%), larger, and encompass genes with established disease associations
  • CNVs account for ~15–20% of diagnoses in intellectual disability and autism spectrum disorder — the highest yield for any single variant class

02Detection Technologies: CMA and WGS

Multiple platforms can detect CNVs, each with distinct strengths and limitations. Understanding the technical basis of each platform is essential for interpreting reported CNVs and recognizing their potential artifacts.

Key Points

  • Chromosomal Microarray (CMA): two main types — array CGH (comparative genomic hybridization) and SNP arrays. SNP arrays additionally detect copy-neutral LOH and segmental UPD
  • WGS for CNV detection: uses read-depth analysis, split reads, and discordant read pairs; superior sensitivity for smaller CNVs and breakpoint resolution
  • CMA limitations: cannot detect balanced rearrangements (inversions, balanced translocations), small variants (<50 kb), repeat expansions, or low-level mosaicism (<10–15%)
  • WGS limitations for CNVs: bioinformatic complexity; coverage uniformity affects sensitivity in GC-rich regions and segmental duplications

03ACMG/ClinGen CNV Classification Framework

The ACMG and ClinGen jointly published the technical standards for interpretation of constitutional CNVs in 2019 (Riggs et al., Genetics in Medicine). This framework uses a scoring system based on five evidence domains to assign one of five pathogenicity classifications, directly analogous to the 5-tier ACMG/AMP variant classification system.

Key Points

  • Five-tier classification: Pathogenic (P), Likely Pathogenic (LP), Uncertain Significance (VUS), Likely Benign (LB), Benign (B)
  • Evidence domain 1: Initial assessment — size of CNV and gene content (coding vs. non-coding)
  • Evidence domain 2: Overlap with established pathogenic or benign CNV regions (OMIM, ClinVar, ISCA/ClinGen, DGV)
  • Evidence domains 3–5: Functional/phenotypic evidence (gene dosage sensitivity, inheritance data, phenotype match)
  • Haploinsufficiency (HI) score and triplosensitivity (TS) score from ClinGen assess how tolerant each gene is to loss or gain of a single copy

04Recurrent Genomic Disorders in Neurogenetics

Recurrent CNVs arise at specific genomic loci flanked by segmental duplications (low-copy repeats) through non-allelic homologous recombination (NAHR) during meiosis. These 'genomic disorders' produce stereotyped phenotypes and account for a substantial fraction of neurogenetic diagnoses.

Key Points

  • 22q11.2 deletion syndrome (DiGeorge/velocardiofacial): ~3 Mb deletion; conotruncal heart defects, palatal abnormalities, developmental delay, schizophrenia risk (1/4,000 births)
  • Williams-Beuren syndrome: ~1.5 Mb deletion at 7q11.23; hypersociability, intellectual disability, supravalvular aortic stenosis; caused by haploinsufficiency of ELN and other genes
  • 1p36 deletion syndrome: most common subtelomeric deletion; severe intellectual disability, hypotonia, seizures, heart defects
  • 15q11–q13: parent-of-origin dependent — maternal deletion → Angelman syndrome; paternal deletion → Prader-Willi syndrome; maternal duplication → autism spectrum disorder

05CNV Reporting and Clinical Communication

Accurate and clinically actionable reporting of CNVs requires consistent use of standardized nomenclature (ISCN/HGVS), appropriate evidence-based classification, and clear communication of clinical implications to referring clinicians and patients.

Key Points

  • ISCN/HGVS nomenclature: report CNV coordinates using a current genome build (GRCh38 preferred); include gene content summary
  • Parental studies: testing parents (inheritance) provides critical evidence — de novo CNVs are ~10-fold more likely to be pathogenic than inherited CNVs
  • VUS CNVs: communicate clearly that VUS cannot be used clinically; offer follow-up parental testing and plan for reclassification review
  • Incidental findings: CMA may reveal clinically significant CNVs unrelated to the indication; pre-test counseling should address this possibility

Quiz Questions

1. Which of the following CNVs would be MOST strongly supported as pathogenic based on ACMG/ClinGen framework evidence?

  1. A.A 50 kb duplication within a known benign population CNV at 1.2% frequency in gnomAD-SV
  2. B.A de novo 500 kb deletion encompassing a ClinGen HI score-3 gene with a matching phenotype✓
  3. C.A 1 Mb duplication inherited from a clinically unaffected parent with no matching OMIM phenotype
  4. D.A 200 kb deletion in a region with no OMIM genes and 3% population frequency

A de novo CNV is ~10-fold more likely to be pathogenic than an inherited CNV. Combined with overlap of a gene with established haploinsufficiency (ClinGen HI score 3) and a clinically matching phenotype, this CNV would accumulate sufficient evidence across multiple domains to be classified Pathogenic under the ACMG/ClinGen framework.

2. What mechanism generates recurrent CNVs at loci flanked by segmental duplications?

  1. A.Non-homologous end joining (NHEJ) during double-strand break repair
  2. B.Non-allelic homologous recombination (NAHR) between flanking low-copy repeats during meiosis✓
  3. C.LINE-1 retrotransposon insertion causing focal amplification
  4. D.Replication fork stalling and template switching (FoSTeS/MMBIR)

Recurrent genomic disorders arise primarily through Non-Allelic Homologous Recombination (NAHR) — a meiotic recombination event between paralogous low-copy repeats (segmental duplications) flanking a genomic region. The high sequence homology between these repeats leads to misalignment, causing recurrent deletions or duplications of the intervening segment with highly consistent breakpoints.

3. According to the ClinGen CNV dosage sensitivity framework, which finding most strongly supports pathogenicity of a deletion CNV?

  1. A.Overlap with a gene that has a ClinGen Haploinsufficiency score of 3 (sufficient evidence for HI) with a matching clinical phenotype✓
  2. B.Overlap with a common population CNV at >0.5% frequency in DGV
  3. C.Inheritance from an unaffected parent
  4. D.Location in a gene-sparse chromosomal region

A ClinGen Haploinsufficiency (HI) score of 3 indicates sufficient evidence that loss of one copy of this gene causes a clinically recognizable phenotype. A deletion encompassing such a gene, combined with a phenotype that matches the expected disorder, provides strong evidence of pathogenicity. Inheritance from an unaffected parent actually argues against pathogenicity (or for reduced penetrance).

4. A CNV is found that overlaps with a region of known parent-of-origin effects. The deletion is found on the maternally inherited chromosome 15 at 15q11–q13. The most likely diagnosis is:

  1. A.Prader-Willi syndrome
  2. B.Angelman syndrome✓
  3. C.15q11–q13 duplication syndrome (autism)
  4. D.Fragile X syndrome

The 15q11–q13 region is subject to genomic imprinting. A maternal deletion of this region causes Angelman syndrome (characterized by intellectual disability, absent speech, seizures, and happy demeanor — due to loss of UBE3A, which is only expressed from the maternal allele in neurons). A paternal deletion of the same region causes Prader-Willi syndrome.

5. A 2.5 Mb deletion at 22q11.2 is identified in a child with conotruncal heart defect, cleft palate, and developmental delay. This most likely represents:

  1. A.1p36 deletion syndrome
  2. B.Williams-Beuren syndrome (7q11.23 deletion)
  3. C.22q11.2 deletion syndrome (DiGeorge/velocardiofacial syndrome)✓
  4. D.Phelan-McDermid syndrome (22q13.3 deletion)

The clinical triad of conotruncal heart defect, palatal abnormality (velopharyngeal insufficiency or cleft palate), and developmental delay is characteristic of 22q11.2 deletion syndrome (DiGeorge/velocardiofacial syndrome). This is the most common microdeletion syndrome, occurring in approximately 1/4,000 births, and is caused by a ~3 Mb deletion at 22q11.21.