Effect Allele Frequency

The Effect Allele Frequency shows how often the allele is found in the population. It is given as a decimal (e.g. 0.33 = 33%).

On Genetic Lifehacks, the effect allele frequency is based on the ALFA global frequency database (Allele Frequency Aggregator) using genetic information from over 1 million people worldwide. You can learn more about ALFA here: https://www.ncbi.nlm.nih.gov/snp/docs/gsr/alfa/#alfa-at-a-glance


Example:

In the screenshot above, the MTHFR rs1801133 effect allele is "A" and the frequency of the allele is 0.33 or 33%.


What can you learn from the effect allele frequency?

The frequency of the effect allele can help to put all of this genetic information into more context for you. A common variant with a modest effect on the function of the gene may not have as great of an effect size.

Here's an example:

If you see a lot of highlighted effect alleles for a topic — say for psychopathy or schizophrenia — you may be wondering how your genes stack up to the rest of the population. If half the world has the same risk allele for schizophrenia, but that only 1% of the population has the disease, it puts into perspective that the genetic susceptibility is just adding a little bit to the risk of a trait or disease.


Calculating the frequency of heterozygous or homozygous:

The effect allele frequency can be used to calculate the frequency of heterozygous and homozygous genotypes using the following equation based on the Hardy-Weinberg principle.

In this example, we will use two alleles, A and G, with A as the minor or less common allele.

We will let:

p = frequency of G

q = frequency of A

Because there are only two alleles, p + q = 1

Thus, if we know that the frequency of A is 0.33, then the frequency of G is 1 - 0.33 = 0.67.


To determine the likely frequency of the different genotypes:

p² + 2pq + q² = 1


Using this equation, we can determine genotype frequency:

  • Homozygous AA is (0.33)2 = 0.11 —> This means 11% of the population has the AA genotype
  • Heterozygous AG is  2×0.33×0.67=0.44 —> This means that 44% of the population has the AG genotype
  • Homozygous GG is (0.67)2 = 0.45 —> This means that 45% of the population has the GG genotype