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SNP Panel Genotype Interpretation Report

The report displays information about the polymorphisms added to the SNP panel, including their identified genotypes and the corresponding interpretation.

To generate this report for a sample, create a report template that includes the "SNP panel interpretation by genotype" block.

The report includes only those polymorphisms that meet the following criteria:

  • the polymorphism has been added to the SNP panel in the report template;
  • the sequencing depth at the polymorphism position is not lower than the coverage threshold for genotypes specified in the report template.

If no matching polymorphisms are found, the following message is displayed: "Specified alleles were not found".

The polymorphisms are displayed in a table with the following columns:

  1. Gene - the name of the gene in which the polymorphism is located.
  2. Location (GRCh38) - the genomic coordinates of the polymorphism (chromosome and position) together with the nucleotide substitution:
  • reference allele > alternative allele - for alternative homozygous, alternative heterozygous, and reference heterozygous genotypes;
  • reference allele = - for the reference homozygous genotype. This notation indicates that no substitution occurs and the variant is represented by the reference allele.
  1. Genotype - the pair of alleles representing the polymorphism genotype:
  • reference allele / alternative allele - for reference and alternative heterozygous genotypes;
  • alternative allele / alternative allele - for the alternative homozygous genotype;
  • reference allele / reference allele - for the reference homozygous genotype.
  1. Exon - the exon number of the transcript in which the polymorphism is located. The following values may be displayed:
  • exon number (or exon range) / total number of exons in the transcript - retrieved from the variant annotation for alternative homozygous, alternative heterozygous, and reference heterozygous genotypes, or from the report template for the reference homozygous genotype;
  • - - indicates that the polymorphism is located outside an exon. The value is retrieved either from the variant annotation or from the report template, depending on the genotype;
  • ref. val. - displayed for the reference homozygous genotype if the Exon field was left empty in the report template.
  1. cDNA Variant (AA Change) - information about the nucleotide and amino acid substitutions. This field is not displayed for the reference homozygous genotype. The following values may be provided:
  • HGVSc - a nucleotide substitution described according to the HGVS nomenclature.
    Format: position + reference allele > alternative allele. The prefixes c. (coding) and n. (non-coding) are used. Example: c.176T>C.
    Hovering over the value displays the full notation including the Ensembl transcript ID, for example: ENST00000559488.7:c.176T>C.
  • HGVSp - an amino acid substitution described according to the HGVS nomenclature.
    Format: p.(three-letter reference amino acid + position + new amino acid). Example: p.(Leu59Pro).
    Hovering over the value displays the short notation using one-letter amino acid codes, for example: p.L59P.
  1. Transcript - the identifier of the main gene transcript from the RefSeq (NM_xxxxxx.x) or Ensembl (ENSTxxxxxxxxxxx) database.
  2. Allele Frequencies - the frequencies of all known polymorphism alleles according to the gnomAD v3 database. Values are displayed as percentages. If no frequency is available for an allele, n/a is displayed.
  3. Coverage Depth - the total number of independent sequence reads for a genome region containing the mutation.
  4. dbSNP - the polymorphism ID in the dbSNP database, displayed as a link to the corresponding page.
  5. A link to the polymorphism position visualization module: .

An interpretation of the corresponding genotype may be displayed below each polymorphism if it was defined in the report template.

Exporting the Report#

The SNP Panel Genotype Interpretation Report can be downloaded as a PDF. To download the report, click in the upper-right corner of the report page.