Variant table

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The results are displayed in the Variant Table. Rows contain the identified variants, and columns contain core annotations for each variant (Variant, Variant type, Class, Genes, Function, Zygosity, Allelic balance, Coverage). However, none of the columns are mandatory, you can choose which ones will be displayed with the "Show/hide columns" icon.

Tip: The column order in the variant table is user-specific, meaning each user can set up own order and visibility of columns.

Moving the mouse over column names containing an info icon will open info pop-ups. The variants can be reordered using other columns by clicking on .

Tabs on the right and on the bottom of the variant table display complementary information. The variant table can be accessed by the user who requested the analysis or by other people belonging to the same group.

variant-table

Description of main functionalities

Columns for Germline samples

  • Variant: The variant’s sequence and genomic location.
  • Variant type: SNV (single nucleotide variant); for INDELs and substitutions, the number of nucleotides affected are shown.
  • (i) User variant classification: custom classification for variants. Custom classification is linked to the variant and will be displayed in other analyses of your group if the same variant is found.
  • Class: Variants are ordered by our pathogenicity classification:
    • 5 = Pathogenic
    • 4 = Likely pathogenic
    • 3 = Uncertain significance
    • 2 = Likely benign
    • 1 = Benign.
  • We reserve classes 5 and 1 for variants that have been annotated as such in ClinVar. If a variant has been annotated as pathogenic (5) or likely pathogenic (4) by ClinVar, this variant will be shown as class 5 or 4 in VarSome Clinical, even if the allele frequency in the population suggests that this variant is unlikely to cause the disease. Note that the variant class refers to how the variant would affect the protein function; a class 5 variant does not necessary need to be the cause of the disease, e.g. if the gene is autosomal recessive and the patient is heterozygous.
  • Overlapping Genes: The name of any gene(s) the variant falls within.
  • Function: The position of the variant with respect to the gene it falls within, and its coding effect (if any).

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  • Gene Symbol: Gene used for annotation and classification of  the variant for ACMG (& AMP for somatic samples)
  • Zygosity:

zygosity

If the variant did not pass the variant caller quality filter, the zygosity is shown in the table as (failed quality/non- genotyped).

  • Allelic balance: Proportion of reads that support the variant.
  • Coverage: Number of reads that align to the variant’s position. For analyses of fastq samples, the blue numbers contain links to JBbrowse, showing the read alignments at the variant’s position.

Extra columns for Somatic samples

  • AMP Tier: Variants are ordered by an aggregate AMP score (see AMP Implementation documentation for more details), from most pathogenic to benign.  Tier I = Cancer with approved drug therapies, Tier II = Cancer but no approved therapy, Tier III = Uncertain Significance, Tier IV = Benign or not related to cancer.
  • AMP Rules: The set of triggered AMP rules are displayed in clickable bubble icons that include each rule’s description and explanation for triggering
    • Sample Metrics:Each icon represents the sample information introduced by the user. They light up when there is data in one of the cancer-related databases matching the variant to the relevant sample characteristic:
      • Cancer type: this highlights any variants for which evidence is found linking to the same cancer type as the sample.
      • Tissue: This will highlight any evidence associating the variant or gene to the sample tissue.
      • Age: This will display the patient's age relative to an age histogram for certain cancer types.
      • Ethnicity: It will report the variant's frequency in the relevant ethnic group.
      • Sex: more than 50% of reported cases across somatic sample databases match the sample’s sex.
      • Variant Allele Frequency: The VAF of this variant in this sample is under 30%, indicating a tumor variant
    • Somatic Samples: Sum of available affected samples from databases included in Cancer Aggregator (ICGC Somatic, COSMIC, CBioPortal, Cancer HotSpots, GDC)

    Tabs

    • Frequencies: If known, Gnomad frequencies for the selected variant and for any other known variants that overlap with it.
    • Clinical: ClinVar and Cosmic annotations for the selected variant nd for any other known variants that overlap with it.
    • Transcripts: Chromosomal location, link to UCSC genome browser, dbSNP (rs number), Refseq transcripts containing the variant, HGVS notation, etc.
    • Genes: Information about the gene(s) affected by the variant, and links to multiple external databases: ExAC genes, Gene expression, Drug-Gene Interaction database (DGI), etc.
      • Cancer Databases: PMKB, CIVIC, CGC, JAX CKB
      • Drugs Databases: PharmGKB, AACT Clinical Trials, DGI, FDA
    • CGD & HPO: Clinical Genome Database (CGD) and Human Phenotype Ontology (HPO) annotations.
    • #Samples: This tab shows the number of samples in which a specific variant has been found. This column is updated over the weekend. The number of homozygotes and heterozygotes in VarSome Clinical for the variants are shown, but only sample IDs of samples analysed by you and your group are reported.
    • Nearby variants: Variants in the genomic neighborhood of the selected variant. This variant list is not affected by the filters applied to the sample.
    • Audit Trail: Shows the record of the actions that have been made from all users of a group on the samples analyzed.

    Some useful icons:

    • Click on this box to get access to your saved filter sets:

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    • Clicking on the filter icon opens the Filters menu where you can manage Filter Sets. To exit the menu, simply press "Esc" on your keyboard.

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    • Click on the arrow icon to see the list of variants selected for export.

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    • Clear search: It is possible to search for a position (eg. chr3 190106073) or for a gene by typing in the Search... box. This will filter the table and show only the results for that position or gene. The Search... box can be emptied by clicking on the Clear icon.
    • Reset order: Clicking on this icon resets the sorting order of the columns to the default (the variants will be ordered by Class).
    • Reset state: Column order can be changed using drag and drop. Clicking on this box shifts back to the original view, with all columns.
    • Filters for custom variant classification
    • Open the Custom Tag creation menu. Custom tags allow you to classify variants using user-defined tags.
    • Show/hide columns: Remove or add columns to the table. This functionality can be used to remove columns that are not relevant for the analysis.

     

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    • Classify variants: add your own classification to a variant.
    • VCF attributes: pop-up window describing the quality details for each software tool used to identify the variants.
    • Transcripts: pop-up window with all the RefSeq transcripts containing the variant. It also shows the location of the variant (intron/exon, amino acid position), its HGVS notation, and genomic function (intronic, exonic, splicing, UTR ...). Canonical transcripts are shown in red.
    • Comments: It is possible to write personal comments about a variant. These comments will be linked to the variant and will be displayed in other analyses. Variants with comments will have an icon in the Chromosome column. Comments are shared only within your group, unless you decide to make your comments public.
    • View in VarSome: link to our free knowledge-base and database aggregator, VarSome.
    • Select for export: Clicking on this box selects the variant for export, and information about the variant can be exported in Word and Excel format ("Export variant list" box)

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    • Gene coverage: a pop-up window showing the average coverage for the selected gene and its different transcripts. Clicking on the nodes will expand or collapse the tree.

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    Also, by clicking on one of the Exons, a new tab will open with a Jrowse(jbrowse.org) window showing the alignment details from the analysis’ bam files. JBrowse is a software tool installed on our secured servers.

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    • Read Alignment: Opens a new tab with a JBrowse representation of the BAM files (more in FAQs: What is represented in JBrowse?)

     

    Red boxes:

    Analysis actions: described here

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    Filtered Variants:

    Download all filtered variants shown in the table (max. 50000) in Excel format. The Excel file also contains information about the filters used to obtain the exported table.

    Description of CNV analyses functionalities

    CNV/SV analysis Variant Table contains the following information:

      • Length: the length in bp of the region considered as a structural variation.
      • Type: deletions, duplications, copy number variants and insertions.
    • Genes: genes overlapping the CNV region.
    • Quality Score: For multi-sample cohort analyses which are run with the  ExomeDepth CNV caller, it is the Bayes Factor: log10 of the likelihood ratio of data for the CNV call divided by the null (normal copy number). For WGS CNV analyses, it is the quality score as given by  DELLY.
      • For CNVs from VCF, provided for annotation only, the Quality Score displays the QUAL value from the VCF (if included).
    • ACMG CNV class and CNV rules: the ACMG CNV classification and the set of triggered ACMG rules. These rules are displayed in clickable bubble icons that include the rule’s description and explanation for triggering.
    • Number of exons: number of exons overlapping the CNV region.
    • Reads  expected, reads observed and reads ratio: these columns contain the values for each CNV of the reads expected, the reads observed, and the read ratio (reads observed / reads expected). 
    • Frequency: frequency of overlapping CNVs in the same genomic region. The gnomAD database is used to get the general population frequencies for a given structural variant. Depending on the type of variant, the frequencies are calculated as follows:
      • Deletions: we use gnomAD variants if they fully overlap with the given variant.
      • Duplications in coding regions: we compare at the gene level and we use those gnomAD variants that encompass the same coding genes as the given variant.
        • Duplications in non-coding regions: we use gnomAD variants if they are at least covering 85% of the variant region.


      CNV tabs

      • Genes: the gene information for all the genes overlapping the CNV region is available at the right side of the window unde the “Genes” tab.
      • Transcripts: A list of all the affected transcript positions that overlap with each CNV is displayed on the right of the Variant Table, under the "Transcripts" tab.



      • ACMG: in this tab we show the ACMG CNV classification and the set of triggered ACMG rules. Click on “Show full detail” to find out the criteria not met.
      • CNV plots: we provide a CNV plot, showing how the observed read depth in the area of the CNV differs from the expected. The CNV plots are generated using a modified version of the ExomeDepth tool. You can find further information regarding CNV visualization.
      • Known CNVs: we display only the relevant CNVs for the classification according to the following criteria: 
        • CNV deletions: we retain those that fully overlap with the given CNV for gnomAD variants. For CNVs coming from clinical sources (Decipher, DBVar, ClinVar CNVs) we use the overlapping CNVs if they are benign and the contained CNVs if they are pathogenic.
        • CNV duplications: we keep only the CNVs encompassing the same coding genes. If the CNV is non-coding, then we retain the CNVs that have at least 85% of overlap.