Summary tab
The Summary tab highlights core variant-related information from other Variant page tabs:
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 . Shown only if not empty.
2) Variant Info
SNV/Indel, MNV (v100.39.0+), 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.
SNV/Indel, MNV (v100.39.0+), mtDNA variant (SNV/Indel), STR:
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),
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
Link to the disease page in MONARCH (100.39.0+)
Phenotype match summary (displayed only for tagged variants):
Number of disease phenotypes matching patient's phenotypes out of total
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 . 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.
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;
