What is variant allele frequency?


Variant allele frequency (VAF) is a measurement used in the genetic testing of tumours. It describes how common a specific genetic change is within a tested tissue sample and is usually reported as a percentage.

Tumours are often tested for genetic changes because these changes can explain why a cancer developed, how it may behave, and which treatments may work best. A genetic change is called a variant, and most cells normally have two copies (alleles) of each gene. Variant allele frequency tells doctors what proportion of those gene copies carry the variant.

For example, a VAF of 50% means about half of the DNA copies tested contain the genetic change, whereas a VAF of 10% means the change is present in fewer cells.

Why is variant allele frequency important?

Variant allele frequency helps doctors understand how widespread a genetic change is within a tumour.

A higher VAF usually means the variant is present in many tumour cells. This may suggest that the change happened early in tumour development or plays an important role in how the cancer grows.

A lower VAF means the variant is present in fewer cells. This can happen when a tumour contains a mix of different cell populations, when the change developed later, or when the sample includes both tumour cells and normal cells.

Even variants with a low VAF can be significant, especially if they affect treatment decisions.

How is variant allele frequency measured?

Variant allele frequency is measured using molecular tests, most commonly next-generation sequencing (NGS). These tests examine thousands to millions of DNA fragments and count how many contain the variant compared to how many do not.

Because these tests are highly sensitive, they can detect genetic changes even when present in only a small fraction of cells.

Does variant allele frequency show how aggressive a cancer is?

No. Variant allele frequency does not measure tumour size, cancer stage, or aggressiveness on its own. Instead, it provides information about how common a genetic change is in the tested sample.

Doctors always interpret VAF together with the tumour type, pathology findings, imaging results, and clinical history.

Does variant allele frequency show whether a genetic change is inherited?

Not by itself. Variant allele frequency cannot reliably determine whether a genetic change is inherited or developed only in the tumour.

In some cases, a VAF near 50% in non-tumour tissue may suggest an inherited variant, but additional testing is required to confirm this.

Can variant allele frequency change over time?

Yes. Variant allele frequency can change as a tumour grows, responds to treatment, or develops new groups of cancer cells. For this reason, repeat testing may sometimes show different VAF values over time.

Why might variant allele frequency be included in my pathology report?

Variant allele frequency is included to help doctors understand how prominent a genetic change is within your tumour. This information can help guide treatment decisions, explain tumour behaviour, and support follow-up testing when needed.

Questions to ask your doctor

  • What genetic changes were found in my tumour?

  • What is the variant allele frequency for those changes?

  • Does the VAF affect my treatment options?

  • Could this genetic change be inherited?

  • Will repeat testing be needed in the future?

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