AION Variant Cards

The following annotations are shown for each analyzed and ranked variant:

For each prioritized variant, either in AION Smoking Guns or AION Clues list, shows the following information is shown:

• AION rank

  AION rank is the main output of our platform. Our prioritization of classified variants in AION is based on obtaining the best matches between 1) patient HPO terms, and 2) HPOs related to rare diseases, associated to genes in which candidate pathogenic variants have been found. Variants are considered pathogenic based on a combination of ClinVar, our implementation of ACMG/AMP guidelines, and ML-based classification values.

  Variants are ranked according to a patient-disease phenotype similarity, associated modes of inheritance for each gene, as well as co-segregation information (when parents VCF files have also been uploaded) and other metrics such as variant tiering. The bigger the phenotype similarity, the more confident we are that a variant or variants (compound heterozygous for example) can explain the patient's disease. The list of HPOs inputted for a Case is taken into account to calculate the p-value for a variant, and variants are ranked/prioritized according to the p-value. Therefore, it is important to provide as much clinical information as possible from a patient, in the form of HPOs, to obtain accurate phenotype similarity values for variant prioritization.

  

• Gene  where the variant is located and related disease are shown in the header of the card, with confidence of the gene-disease-moi association and link to the source. Note! When there are multiple confidences for the same gene-disease-MOI association within the same source, AION visualises the highest confidence one.

  

• Classification

  Available classification for a variant is displayed according to 3 different sources:

  • ClinVar: ClinVar database variant classification. If a variant has been described in ClinVar, clicking on the link will open the ClinVar webpage for the described variant, with extensive information on variant evaluation, submitters, etc. A variant can be classified as Pathogenic (P), Likely Pathogenic (LP), Variant of Uncertain Significance (VUS), Likely Benign (LB) or Benign (B), among other values. Conflicting interpretations are also displayed (CI). When the variant  has not been described in ClinVar "NO EVALUATION" is displayed.

    Notice that the updated category “Conflicting classifications of pathogenicity” will remain to be shown as “Conflicting interpretations of pathogenicity” in the user interface in order to facilitate the user filtering by this conflicting category in a uniform and consistent way under the same category. 

  • AION DB: Previous classifications done by users from your institution on this variant will be shown.

  • ACMG: ACMG/AMP variant classification has been implemented in AION following the ACMG/AMP variant classification standards. The application of all criteria can be modified by the user, changing the overall ACMG/AMP classification. A variant can be classified as Pathogenic (P), Likely Pathogenic (LP), Variant of Uncertain Significance (VUS), Likely Benign (LB) or Benign (B). Conflicting interpretations are also displayed (CI).

    AION applies ACMG/AMP guidelines taking only into account the criteria that can be deduced from the VCF files. That means that some variants may be initially classified as VUSs if additional criteria that are not related directly to the variant are not assessed manually by the user.

  • AION Predictor: This score displays the output of our Classifier Machine Learning-trained algorithm. The Classifier uses multiple variant properties and its underlying genomic region to classify a variant, such as evolutionary prediction scores, splicing prediction scores or variant frequency in healthy population databases as an input. Based on this score, the algorithm provides a predicted variant classification:

    • 0% - 15% = Benign

    • 15% - 40% = Likely benign

    • 40% - 60% = VUS (Variant of Unknown Significance)

    • 60% - 85% = Likely pathogenic

    • 85% - 100% = Pathogenic

    • Rescued = Variants brought to the prioritized variants list due to the fact that they are a partner with another variant already prioritized (Compound heterozygous).

• Disease symptoms are shown, highlighting their overlap with the patient’s symptoms. Total phenotypical overlap is shown in dark grey, while partial overlap shows an additional dashed line around the symptom.

  
  

• Inheritance pattern. This field displays the OMIM ID candidate genetic disease as well as the associated inheritance pattern/s, as prioritized by AION.

• Segregation: Segregation in trio family. If no parents are uploaded, all variants will display "No data". Also a possible AION detected compound heterozygosity with another variant will be highlighted here.

• Zygosity: Patient's variant zygosity (heterozygous, homozygous), as a reflection of genotype data in Annotations. Reference and alternative alleles.

• Variant effect are shown along with:

  • cDNA change, exon/intron location, and reference transcript (Ensembl).

  • Protein change, variant type (e.g missense, splice region variant) and reference transcript (Ensembl). Variant type is colored in red, orange or blue to denote the variant type impact on protein (red: high, orange: moderate, blue: low). Clicking on Ensembl transcripts redirects users to Ensembl webpage, to show several informations related to each protein/mRNA isoform.

• Location: Chromosome and Genomic reference location (in the reference genome indicated in analysis information section.

• Frequency displays the alternate allele frequency for the variant of interest.

If the variant is found in the internal variant database, then information will be shown related to the internal frequency and past interpretations. See more details in the internal variant database page.

Variant Visualization

All variants have a link to the IGV desktop application to allow visual exploration of the genomic data. To be able to visualize the data you should have the IGV desktop application open with the corresponding reference genome and relevant BAM files. Additionally, port listening must be enabled and configured to the default port (60151) in the Advanced tab of the View > Preferences window (refer to IGV for more information).