Genome Explorer

Genome Explorer vs Genome Explorer Plus

Condition

the disease, trait or medication reaction associated with the genetic variant

Interpretation

an indication of whether all available scientific studies and clinical data support the association between the variant and the condition

'Pathogenic' and 'Likely Pathogenic' indicate support for the association

'Benign' and 'Likely Benign' indicate that the variant may not be associated with the condition

Review Status

an indication of the amount of confidence for the Interpretation

Four stars = highest confidence that the Interpretation is correct

Half of one star = lowest confidence that the Interpretation is correct

this usually occurs when there is only one study about the association between the variant and the condition and therefore the Interpretation is based only on a single study

References

clickable link to each journal article that has been published about the association between the variant and the condition

Links

clickable links that take you directly to additional information (ClinVar) for each variant

Will I be able to understand the genetic data that appears in Genome Explorer and Genome Explorer Plus?

What's the difference between Genome Explorer and Genome Explorer Plus?

Why is there missing data for some genetic variants?

When I search for a gene, why do the results show a different gene?

Most gene names have aliases (also known as synonyms). For example, the BRCA1 gene is also known as BRCC1, BROVCA1, FANCS, PNCA4, PSCP and RNF53. Each of those names is an alias for the same gene. This can get pretty confusing!

Genome Explorer takes this into consideration and makes it easy to search using any alias. Simply search for any alias the gene is known by and Genome Explorer will always know what gene you are referring to.

For example, if you search for FANCS, Genome Explorer will know this is the same as the BRCA1 gene. The search results will show all of your data that's associated with the BRCA1 gene.

It's also important to point out that if you search for FANCS, the results will not show 'FANCS' in the Gene column. Instead, BRCA1 will appear. This is because BRCA1 is the most widely used name for this gene. (The most widely used gene name is also known as the HGNC Approved Gene Symbol.)

So if you search for a gene and a different gene name appears, it's because each name is an alias for the same gene. You can verify gene aliases at HGNC's GeneNames.org.

Why does Genome Explorer show data that I can't find in my data file?

Some data files may not contain a rsid (also known as a rs#) for a variant. Instead, the file may identify the variant simply by it's chromosomal coordinate or the file may use an alternative identification system. Genome Explorer is very advanced and if a data file does not include a rsid for a variant, Genome Explorer will try to add this information.

For example, 23andMe files identify some variants by an i# instead of a rsid. While the i# is an ID system used only by 23andMe, the rsid is the ID used by all scientists throughout the world. Because the rsid is universally recognized as the standard nomenclature for variant identification, Genome Explorer will always try to indicate the rsid for a variant even if the original data file doesn't include the rsid.

While Genome Explorer always tries to assign a rsid to a variant, sometimes this is not possible. For example, a rsid may not appear for a variant because a rsid has not yet been established for that specific variant.

When you see a condition (disease, trait, medication reaction, etc. ) in Genome Explorer Plus, it doesn't mean you have an increased risk for that condition.

When a condition appears in Genome Explorer, it means that the genetic variant listed in that row has been associated in scientific research with that condition. Whether your genetic data indicates that you are at risk of that condition will depend upon the interpretation of your raw genetic data. Your raw genetic data is located in the 'Genotype' column.

Example:

• If variant rs123 is associated with Cystic Fibrosis, anytime data contain genetic testing results for rs123, even if the results indicate no-risk, Genome Explorer will include rs123 and will show that this variant is associated with the condition 'Cystic Fibrosis.'
• On a technical level, if rs123 has reference allele C and alternative allele T then this means that Cystic Fibrosis risk is likely associated with the "T" allele. If the genetic testing results shown in the 'Genotype' column is 'CC' then there is no risk of Cystic Fibrosis due to variant rs123. But if the Genotype column is 'CT' or 'TT' then there may be a risk of Cystic Fibrosis.

Get help understanding your genetic data: Use the Genetic Counseling app to speak with a genetic counselor.

Genome Explorer does not perform any analysis about whether you do or do not have a risk for a condition. Because of this, Genome Explorer will not state that you are or are not at risk for any condition. Only the apps in the 'Health' category of the App Market provide analysis as to whether you are likely to be at increased risk of a condition.

When it appears in Genome Explorer, the term 'Pathogenic' is determined only by the variant, not by your genetic data. Everyone's Genome Explorer that lists that same variant will always show the same data in the interpretation column.

For example, if person A and person B both take 23andMe's DNA test and then they both use Genome Explorer to explore their DNA data, they will have the same list of genetic variants (because 23andMe performs the same test for everyone). While the results for each genetic variant will be unique between person A and person B, the list of variants will be exactly the same.

Since person A and person B will have the same list of variants, they will also have the same information in the 'Interpretation' column of their Genome Explorer. This is because the information in the Interpretation column is associated with the variant.

If 'Pathogenic' appears in the Interpretation column, this is because researchers have identified the variant as being associated with the condition. This is why the term 'Pathogenic' is used. The term Pathogenic does not mean that you have the variant or that this variant is harmful to your health.

The word 'Interpretation' and all the terms in that column such as 'Pathogenic' are official terms obtained directly from the NIH's ClinVar database. Please see the table at the end of this section for more information about the meaning of the terms in the Interpretation column.

Have a question about your DNA data? Use the Genetic Counseling app to get answers.