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PubMed This is a summary of 16 peer-reviewed journal articles Updated
Medical Genetics

Diagnostics & Pathology: Understanding Your CMA Report

At a Glance

Distal 16p11.2 microdeletion is usually identified with a chromosomal microarray because the missing DNA is too small for a standard karyotype to see. A genetics professional should interpret the report’s coordinates, genome version, size, copy number, and any uncertain finding.

Understanding a genetic report can feel like learning a new language. To identify a diagnosis of Distal 16p11.2 (BP2-BP3) microdeletion, doctors use a common first-tier copy-number test called a Chromosomal Microarray (CMA) [1]. Because this specific deletion is so small—typically around 220 kilobases (kb)—it is often invisible under an older, standard test called a karyotype [2][3].

Why Microarray is Commonly Used

Think of a karyotype like a satellite photo of a city from 50 miles up. You can see the big highways (chromosomes), but you can’t see if a single house is missing [3]. A microarray, however, is like a street-level view. It can zoom in to detect the loss of very small pieces of DNA that a karyotype would miss [2].

For the distal BP2-BP3 deletion, the missing piece is “submicroscopic,” meaning it is too small to be seen with a microscope and requires the molecular “zooming” of a CMA [3][4].

How to Read Your CMA Report

When you look at your laboratory report, you are looking for a few specific “landmarks” to ensure you are focusing on the correct region. However, patients should rely on the laboratory’s interpretation and a genetics professional rather than self-diagnosing from coordinates alone:

  1. The Coordinates: The report will list a string of numbers. For the distal BP2-BP3 region, these are usually found around 28.8–29.0 Megabases (Mb) on chromosome 16 [1][4].
  2. The Genome Build: Genetic coordinates change slightly depending on which “version” of the human genome map the lab used. Look for hg19 (also called GRCh37) or hg38 (GRCh38). Always use the coordinates provided in your specific report, as they are tailored to your DNA [5].
  3. The Size: You should see a size of approximately 220 kb, though it can range from 206 kb to 244 kb depending on the individual and the laboratory [1][6][7].
  4. Copy Number: The report should indicate a copy loss or a copy number of 1 (instead of the usual 2) [5].

Understanding “Variants of Uncertain Significance” (VUS)

Sometimes, a microarray finds a copy-number change (a deletion or duplication), but science doesn’t yet know if that change causes health problems. This is called a Variant of Uncertain Significance (VUS) [8][9].

  • Don’t Panic: Having a VUS is very common [10][11].
  • The “Second Hit” Connection: In some cases, a patient may have the BP2-BP3 deletion (which is clearly “pathogenic” or disease-causing) and a separate VUS. If a patient’s symptoms are much more severe than expected, doctors may look more closely at that VUS to see if it acts as a “second hit” [1][12].
  • Next Steps: A VUS should not be used to make medical decisions on its own [13]. Direct families to the testing laboratory or genetics professional for reinterpretation policies rather than assuming it requires a recheck on a rigid schedule [14].

Confirming the Diagnosis in Parents

Because this deletion is small, if a parent had a normal karyotype years ago, it does not mean they don’t have the deletion [2]. To know for sure if the deletion was inherited or occurred de novo (for the first time), parents must also be tested using a microarray or another high-resolution method [15][2]. Establishing this “segregation” (who has the variant in the family) is one of the best ways to help doctors understand the diagnosis [9][16].

Common questions in this guide

Which test is usually used to find a distal 16p11.2 deletion?
A chromosomal microarray, or CMA, is commonly used as a first test because it can detect very small missing pieces of DNA. A standard karyotype may not show this deletion because it is usually only about 220 kilobases in size.
What should I look for on a CMA report for this deletion?
The report may describe a copy-number loss on chromosome 16 in the distal 16p11.2 region, often near 28.8–29.0 megabases. It may list a deletion of about 220 kilobases, a copy number of 1, and the genome version used, such as hg19 or hg38. Use the laboratory’s interpretation rather than trying to diagnose yourself from coordinates.
Does a VUS on my report mean I have another genetic condition?
Not necessarily. A variant of uncertain significance means there is not enough evidence to know whether the finding affects health, so it should not guide medical decisions by itself. A genetics professional or laboratory may review it again as knowledge changes, especially if symptoms are more severe than expected.
Can a normal karyotype in a parent rule out the deletion?
No. The distal 16p11.2 deletion can be too small for a standard karyotype to detect. Parents generally need a chromosomal microarray or another high-resolution test to determine whether the deletion was inherited or occurred for the first time in the child.
Why do hg19 and hg38 matter on a genetic report?
hg19 and hg38 are different versions of the human genome map, so the same DNA region can have slightly different coordinates in each version. The genome version helps the genetics team interpret the exact start and end points reported by the laboratory.
Can the size of the distal 16p11.2 deletion vary?
Yes. Many reports describe a deletion of about 220 kilobases, but reported sizes can vary, including roughly 206 to 244 kilobases. The laboratory’s interpretation and the exact coordinates in the report are more important than comparing the number alone.

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References

References (16)
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    Evaluation of 100 Dutch cases with 16p11.2 deletion and duplication syndromes; from clinical manifestations towards personalized treatment options.

    Vos N, Kleinendorst L, van der Laan L, et al.

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    Phenotypes Associated with 16p11.2 Copy Number Gains and Losses at a Single Institution.

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    Coexistence of a Novel OCRL Variant and a Pathogenic 16p11.2 Deletion in a Patient with Renal and Neurodevelopmental Manifestations Suggestive of Atypical Dent Disease Type 2-A Case Report.

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    The Importance of Familial Co-segregation in the Classification of a Novel PKD1 Variant Associated With Autosomal Dominant Polycystic Kidney Disease.

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This page is for informational purposes only and does not constitute medical advice. It explains how a CMA report may describe a distal 16p11.2 deletion, but a genetics professional or laboratory should interpret your specific results.

Guide contents Distal 16p11.2 microdeletion syndrome
Research & Literature
04 The Metabolic Factor 06 Management, Surveillance & Building Your Care Team