I'm interested in FinnGen rare variant phenotypes
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The FinnGen project is fortunate to have >116k rare coding variants included, many of which are variants specific to the . The section describes the design and contents of the genotyping chip in more detail.
One advantage of FinnGen is that Finnish clinicians can use FinnGen to check variants they may have found in screening Finnish families to help determine if they are causative. Since these are Finnish-specific variants, they are often not found in more international resources such as ClinVar.
Variants can be classified by their frequency:
Common variant refers to variants > 1% and these will be most commonly found as imputed variants.
Low-frequency variant refers to variants with 0.1-1% frequency in the population. These are usually run on the chip but sometimes are common enough that they may also be .
Rare variant usually refers to variants with <0.1% frequency in the population. These are usually available only in chip data.
(Ultra-rare variants are usually not present and FinnGen does not run gene-level burden tests such as SKAT-O. You can check for burden information of ultra-rare variants in UKBB, although this does not contain FinnGen data, it will give you an idea of the values in other populations.)
Which tools are available depend on the frequency of the variant. Below is a map of tools.
Data availability:
Green boxes =
Red boxes = .
Currently, to work with rarer variants you will need red-level Sandbox access.
Using Sandbox requires red-level access.
More about and Chip association browser .
If you are interested in all the coding variants in a particular gene, you can go to and then just type in the name of your gene. At the bottom, you will see all the imputed variants and any associations they may have to FinnGen phenotypes. Here is what is shown for TSHR:
Check genotyping quality via the . (You can find all the cluster plots from the , but you will not be able to fix the calls or run a phenotypic analysis without red-level access.) Or use the to view cluster plots and to fix calls manually.
Look at your variant in the public resource and check that it has been seen in Finland and what its allele frequency is. This can help you estimate if you have the correct number of heterozygotes (Finnish allele frequency from Gnomad v2 = roughly the number of copies/hets for a rare or low frequency variant)
Run with to see which medical codes and FinnGen endpoints the variant is associated with. Use of Cohort Operations needs no coding skills. The other option to explore medical codes and FinnGen endpoints association is to run a PheWAS (see the section and note also that we have a section on ). Running PheWAS requires some experience with R programming.
See also describing the most common workflows researchers are conducting in the Sandbox with the FinnGen. The methods described for genotype variant analysis suits also for exploring rare variants. These methods need no programming skills.
