Repeat Expansion Variant Table and Cards

Repeat Expansion Variant Table

The Repeat expansion analysis variant table contains the following information:

• Position: chromosome and position of the repeat expansion.
• Display repeat unit: display repeat unit familiar to the clinician. 

• Repeat unit: repeat unit in the reference orientation.
• Pathogenicity: repeat expansions can be classified as:

• • • Pathogenic: the number of repeats detected in the sample is equal to or greater than the minimum number of pathogenic repeats.
    • Uncertain Significance: the number of repeats detected in the sample is greater than the maximum normal number of repeats but less than the minimum number of pathogenic repeats, or the minimum pathogenic and maximum normal values are not available in gnomAD STRs.
    • Benign: the number of repeats detected in the sample is smaller than or equal to the normal number of repeats.

• Genes: in which gene the repeat expansion has been found.
• Sample repeats: number of repeats observed in the allele.

• MIN pathogenic repeats: minimum number of repeats needed to consider the variant pathogenic available in gnomAD STRs.

• Normal MAX repeats: maximum number of repeats allowed to call the variant as normal available in gnomAD STRs.
• Ref. genome repeats: number of repeats in the reference genome.

• Zygosity
• Filters: VCF filters.

Dynamic Filters

The repeat expansion table can be seamlessly filtered by pathogenicity verdict, repeat unit and genomic position. 

Repeat expansion cards

• Variant: general variant information, region browser, sample view and gnomAD STR cards.

The gnomAD STR card will display the following summary information:

• • the disease associated with the locus and the minimum number of pathogenic repeats

The gnomAD STR component provides detailed information for each locus, including:

• • Gene: The gene associated with the STR.
  • Position: Whether the STR is located in a coding or intronic region.
  • Reference Region: The genomic coordinates of the reference region.
  • Locus Structure: A regular expression describing the structure of the locus, including the primary disease-associated repeat unit and any adjacent repeats. This is defined using ExpansionHunter.
  • Repeat Unit: The specific repeat motif associated with the STR.

In addition, the resource includes:

• • A table listing associated diseases, corresponding OMIM IDs, mode of inheritance, and pathogenic repeat ranges.
  • A histogram in the gnomAD browser showing the global allele size distribution for the main disease-associated repeat unit. 

• Gene: it contains the same gene cards as the ones displayed under the gene level of the main analysis (small variant table).