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Allele Frequency Calculator

Created by Łucja Zaborowska, MD, PhD candidate
Reviewed by Steven Wooding
Last updated: Jan 18, 2024


The allele frequency calculator allows you to compute your chances of carrying a gene that may cause a specific recessive disease in your offspring.

Our tool is based on the Hardy-Weinberg equilibrium equation.

Still feeling confused? 🤯

Follow our article below to discover what is a gene pool, what are autosomal recessive diseases/disorders, and how they can be inherited. We'll also go one step further - we'll teach you how to find allele frequency in the population and calculate gene frequency.

If you'd like to calculate the phenotype/genotype frequency of certain alleles or learn how to calculate allele frequency in the next generation, try:

And if you are interested in the technique used to effectively see those genes, check our PCR annealing temperature calculator! (You'll find there some more information on the topic, too!) 🎛️

What is allele frequency?

Allele frequency describes how often a particular allele can be found in a population. With the allele frequency, you can calculate the chances that you and your partner are carriers of a genetic disease that may affect your children.

The frequency of particular alleles is higher among people in the same family.

💡 Allele itself is a variant of a gene. Every gene has two variants, that is two alleles. One of the alleles is always inherited from the mother, the second one comes from the father.

💡 Gene is a part of our genome that describes a single trait of our bodies. Genes serve as instruction book for our body's cells.

Why is it important?

Having two alleles of every gene is one of Mother Nature's most ingenious ideas - when one of the alleles is damaged or doesn't work correctly, we always have another copy to replace it with.

Of course, it doesn't always work this way:

  • Both copies of a gene might be broken - that's when the recessive diseases happen 🌟 (we created this calculator for this type of situation).

    • For example, cystic fibrosis.
  • One copy of a gene is broken, but this particular allele is dominant towards the second one and overruns it. That's when dominant diseases happen.

    • For instance, Huntington's disease.
  • Sometimes, only one allele of a gene works, and the second one is turned off on purpose. One of these situations is called the parental imprinting.

    • For example, Prader-Willi syndrome.

How to use the allele frequency calculator?

Our allele frequency tool allows you to calculate the chances of being a carrier of a certain genetic trait or a recessive disease. All you need to know for this calculation is the frequency of the disease in the population, given either as a percentage (%) or a proportion (1 in 10000 people).

You may also use the following definitions:

  • p — frequency of the wild (healthy) allele.

  • q — frequency of the mutant (sick) alllele.

  • — frequency of people with the disease in the population (2 mutant alleles).

  • — frequency of people without the disease in the population (2 healthy alleles).

  • 2pq — frequency of people without the disease in the population (1 mutant, 1 healthy allele).

💡 Carrier is a person that has only one impaired allele of a certain gene - this person usually doesn't get sick, but may pass on the impaired version of the gene to their children. If the second parent is also a carrier of the same disease, the child will probably suffer from this disorder.

We prepared a shortlist of the most common recessive diseases, so you don't have to look for them any further!

Remember, different populations tend to have completely incomparable pules of genes — the sets of all genes in a given population. The prevalence of certain diseases might be completely different than in the general population!

Disease

Prevalence

Albinism

1 in 10,000 in the general population

Cystic fibrosis

1:2,500 in the Caucasian population

Harlequin-type ichthyosis

1 in 300,000 in the general population

Phenylketonuria

1:15,000 in the Caucasian population

Sickle cell anemia

1:600 in the African-American population

Tay Sachs

1:3,600 in Ashkenazi Jewish population

How to calculate allele frequency?

Our carrier frequency calculator uses the following equation:

p² + 2pq + q² = 1

where:

  • — Frequency of people who own two healthy alleles.
  • 2pq — Frequency of people who own one healthy and one impaired gene: the carriers.
  • — Frequency of people who own two impaired genes: the people with the disease.

Let's follow it with an example:

A patient came to our office - his wife is a known carrier of a certain disease. He wants to know what's the probability that he's a carrier too; the disease we're calculating affects 1 in 1,000,000 people.

1:1000000 = 0.000001

q² = 0.000001

q = 0.001

p² + (2 × p × 0.001) + 0.000001 = 1

p² + 0.002p - 0.999999 = 0

Here we need to use the quadratic formula solver and the delta equation: Δ = b² − 4ac.

p can be equal to -1.0015 or 0.9985. Of course, we need to choose the positive result 😉(the negative one is impossible).

Let's calculate the carriers' prevalence:

2pq = 2 × 0.001 × 0.9985 = 0.001997

1 / 0.001997 = 501

The probability that our patient is a carrier is equal to 1:501.

What is the Hardy-Weinberg equation?

In fact, this tool is a Hardy-Weinberg calculator: we use this equation to calculate the frequency of alleles in the population.

p2+2pq+q2=1p^2 + 2pq + q^2 = 1

In the typical description of this formula, we'll find the following descriptions:

  • 11 — Whole population that owns a certain gene;
  • p2p^2 — homozygous dominant (AA);
  • 2pq2pq — heterozygous (Aa); and
  • q2q^2 — homozygous recessive (aa).

What does it really mean?

  • The dominant allele is the one which a trait is almost always visible. We usually mark these alleles as A. Only one dominant allele is enough for certain characteristics to appear. Curly hair is one of the popular dominant traits.

  • The recessive allele is the gene of the lesser strength. We usually mark them as a. A given trait is only visible if both of the alleles in the organism are recessive. Straight hair is an example of a recessive trait.

  • Homozygous means that the cell contains two copies of the same gene, two alleles of the same strength. This combination might be dominant: AA or recessive: aa.

  • Heterozygous means that there are two different copies of a gene. This mix should be marked as Aa.

💡 Our Hardy-Weinberg equation calculator works, because all the people that suffer from a recessive disease can be described as aa; we also know that all the carriers in the population can be described as Aa.

Take a look at our blood type calculator to find out how it works in practice — you may also discover what blood type your baby will have! 👶 🅱️🅰️🆎

FAQ

How do you calculate P and Q allele frequency?

You can calculate the frequency of P and Q by counting the number of each type of allele and subsequently dividing them by the total number of alleles (so the sum of both).

What do P and Q mean in allele frequency?

In the Hardy-Weinberg equilibrium equation for determining allele frequency, p represents the dominant allele, expressed as A, whereas q stands for the recessive allele a.

How to calculate minor allele frequency?

You can calculate the minor allele frequency in the same way you would calculate any other allele frequency with the Hardy-Weinberg equilibrium equation. By calculating the minor allele frequency, you will get information about the frequency of the second most common allele in the population.

How do you find the allele frequency of four alleles?

To determine the allele frequency of four alleles:

  1. Count the number of the allele of interest.

  2. Divide it by the whole number of alleles.

  3. Repeat the same for each allele of interest, respectively.

  4. Once you have determined the frequency of all alleles, make sure that the result is in accordance with the Hardy-Weinberg equilibrium equation for 4 alleles:

    p + q + r + s = 1

If you want to go on and determine genotype frequency, you need to take the equation to the power of two:

(p + q + r + s)² = 1

With four alleles, you will have 10 genotypes:

p² + 2pq + 2pr + 2ps + q² + 2qr + 2qs + r² + 2rs + s² = 1

What are the allele frequencies if 1% of people have a disease?

If we want to know the allele frequency of a disease that occurs in 1% of the population, you need to take the following steps:

  1. Know that the percentage of people with the disease is the value for in the Hardy-Weinberg equation for genotype frequency:

    p² + 2pq + q² = 1

  2. Take the root of q² to determine the allele frequency of the mutated allele, which is 0.1.

  3. Subtract this value from 1, which is the total allele frequency, in order to obtain the value of p. This calculation is based on the Hardy-Weinberg equation for allele frequency:

    p + q = 1

  4. You will obtain the following result:

    p = 0.9 and q = 0.1

Łucja Zaborowska, MD, PhD candidate
Frequency of the disease in the population
Given in:
Proportion
Occurrence of the disease: 1 in..
×% = 1 in × people
Allele frequency
Healthy allele frequency (p)
Mutant allele frequency (q)
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