Summary tab

The Summary tab highlights core variant-related information from other Variant page tabs:

• Clinical Significance tab (Variant Info, In silico Prediction, Gene's related diseases, Clinical significance),

• Quality tab (Quality),

• Population Statistics tab (Population Summary),

• Evidence tab (Variant Interpretation, ACMG Classification, Pathogenicity).

Each of the Summary tab cards has a button linking to its original location on the Variant page where you can see more details and/or edit the evidence.

Let's look closer at each of the cards:

1) Variant Interpretation

Notes added automatically or manually in the Evidence tab. Shown only if not empty.

2) Variant Info

• Sequence variant (SNV/Indel), mtDNA variant (SNV/Indel): main effect*,* gene symbol, if available - HGVS descriptions on coding DNA and protein levels.

* CNV (DEL/DUP): CNV length, variant type, number of genes involved, list of gene symbols. If the gene list is partial, you may hover over it to see the full list.

3) Quality

• Sequence variant (SNV/Indel), mtDNA variant (SNV/Indel), STR:

  • variant caller

  • sample name

  • zygosity

  • depth of coverage

  • percentage of alternative allele reads

  • overall variant quality

• CNV (DEL/DUP):

  • variant caller

  • sample name

  • zygosity

  • overall variant quality

4a) Population Summary

Population statistics from gnomAD (calculated for the combined gnomAD population including both exome and genome samples):

• Total AF - overall alternative allele frequency,

• Allele count - Counts of alternative allele (or Homoplasmy Count for mtDNA variants),

• Hom/Hemi count - Counts of alternative allele in homozygous or hemizygous state (or Heteroplasmy Count for mtDNA variants),

• Max AF - the highest alternative allele frequency among gnomAD populations;

Population statistics from organization databases (if available):

• Allele count - Counts of alternative allele,

• Hom/Hemi count - Counts of alternative allele in homozygous or hemizygous state.

4b) STR repeats distribution

STR repeats distribution displays allele counts in gnomAD and 1000 Genomes Project, as well as gnomAD pathogenicity ranges.

5) Gene's related diseases

• Number of disease connections for the gene in the Emedgene knowledge base

• Name of the selected disease

• Inheritance mode(s) of the selected disease

• GenCC validity badge (100.39.0+) When the selected disease has one or more entries in the GenCC (Gene Curation Coalition) database, a badge representing the highest-level gene–disease validity classification is displayed next to the disease’s inheritance mode. If multiple GenCC entries exist for the same gene–disease connection, a “+n” indicator appears beside the badge. Hovering over this indicator reveals the additional classifications and their sources.

• Links to the gene–disease connection source(s) for the selected disease:

  • OMIM

  • Academic papers included in the Emedgene knowledge graph

  • CGD

  • ClinVar

  • Orphanet

  • GenCC (100.39.0+)

  • MONARCH (100.39.0+)

• Phenotype match summary (displayed only for tagged variants):

  • Number of disease phenotypes matching patient's phenotypes out of total

  • List of disease phenotypes with match levels indicated

6) Pathogenicity

Here you can see user-assigned variant Pathogenicity, change it or select one from the dropdown if it's empty.

7) Clinical significance

This card highlights previous pathogenicity classifications in public and your private variant databases including Curate. Each classification source is represented by one badge. Uncertain and Other classifications are only shown if there are no Benign/Likely Benign and/or Pathogenic/Likely Pathogenic classifications of this variant in a particular database.

8) ACMG Classification

Showcases ACMG tags assigned to the variant and the resulting classification.

• Sequence variant (SNV/Indel), mtDNA variant (SNV/Indel)

  The final class, the criteria used and the score.

• CNV (DEL/DUP)

9) In silico Prediction

Overall estimations of in silico prediction results.

• Small variant (SNV): Missense Prediction, Conservation, Splicing Prediction;

• Small variant (Indel): Conservation;

• mtDNA (SNV/Indel): Missense Prediction;

• CNV (DEL/DUP), SV, STR: not available.