> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/summary_section.md). # Summary tab The **Summary** tab highlights core variant-related information from other [**Variant page**](/emedgene/emedgene-analyze-manual/variant_page/variant_page.md) tabs: * [**Clinical Significance tab**](/emedgene/emedgene-analyze-manual/variant_page/clinical_significance_section.md)**:** [**Variant Info**](#variant-info), [**In silico Prediction**](#in-silico-prediction), [**Gene's related diseases**](#genes-related-diseases), [**Clinical significance**](#clinical-significance) **cards** * [**Quality tab**](/emedgene/emedgene-analyze-manual/variant_page/quality_section.md)**:** [**Quality card**](#quality) * [**Connected variants** **tab**](/emedgene/emedgene-analyze-manual/variant_page/connected-variants-tab.md)**: Connected variants card** * [**Population Statistics** **tab**](/emedgene/emedgene-analyze-manual/variant_page/population_statistics_section.md)**:** [**Population Summary card**](#population-summary) * [**Evidence tab**](/emedgene/emedgene-analyze-manual/variant_page/evidence_section.md): [**Variant Interpretation**](#variant-interpretation), [**ACMG Classification**](#acmg-classification), [**Pathogenicity**](#pathogenicity) **cards**

Each **Summary tab** card links to its original location on the **Variant page** where you can review full details.

**Summary tab cards** link to their source tabs.

Let’s look more closely at each card. *** ## Variant Interpretation Notes are added automatically or manually in the [**Evidence** **tab**](/emedgene/emedgene-analyze-manual/variant_page/evidence_section.md). They appear only when present.

*** ## Variant Info **SNV/Indel, MNV (v100.39+), mtDNA SNV/Indel** {% columns %} {% column width="50%" valign="middle" %}

{% endcolumn %} {% column width="50%" %} * Main effect * Gene symbol * HGVS descriptions at the coding DNA and protein levels {% endcolumn %} {% endcolumns %} **DEL, DUP, LOH/ROH** {% columns %} {% column width="50%" valign="middle" %}

{% endcolumn %} {% column width="50%" %} * Variant length * Variant type * Number of genes involved * Gene symbol(s) {% hint style="info" %} Hover to see the full gene list. {% endhint %} {% endcolumn %} {% endcolumns %} **INS** {% columns %} {% column width="50%" valign="middle" %}

{% endcolumn %} {% column width="50%" %} * Variant length * Variant type * Main effect * Gene symbol {% endcolumn %} {% endcolumns %} **TRA (v100.41+)** {% columns %} {% column width="50%" valign="middle" %}

{% endcolumn %} {% column width="50%" %} * Variant type * Main effect * Number of genes involved * Gene symbols {% endcolumn %} {% endcolumns %} **INV (v100.41+)** {% columns %} {% column width="50%" valign="middle" %}

{% endcolumn %} {% column width="50%" %} * Variant length * Variant type * Main effect * Number of genes involved * Gene symbol(s) {% endcolumn %} {% endcolumns %} **BND (v100.41+)** {% columns %} {% column width="50%" valign="middle" %}

{% endcolumn %} {% column width="50%" %} * Variant type * Main effect * Gene symbol {% endcolumn %} {% endcolumns %} **STR** {% columns %} {% column width="50%" valign="middle" %}

{% endcolumn %} {% column width="50%" %} * Total length of the repeat region * Gene symbol * HGVS descriptions at the coding DNA and protein levels {% endcolumn %} {% endcolumns %} **Haplotype** {% columns %} {% column width="50%" valign="middle" %}

{% endcolumn %} {% column width="50%" %} * Haplotype name * Individual genotype * Number of genes involved * Gene symbol(s) {% endcolumn %} {% endcolumns %} *** ## Quality **SNV/Indel, MNV (v100.39+), mtDNA SNV/Indel, STR** {% columns %} {% column width="50%" valign="middle" %}

{% endcolumn %} {% column width="50%" %} * Variant caller badge * Zygosity per sample * Depth of coverage per sample * Percentage of alternative allele reads per sample * Overall variant quality per sample {% endcolumn %} {% endcolumns %} **DEL, DUP, LOH/ROH, INS, TRA (v100.41+), INV (v100.41+), BND (v100.41+), Haplotype** {% columns %} {% column width="50%" valign="middle" %}

{% endcolumn %} {% column width="50%" %} * Variant caller badge * Zygosity per sample * Overall variant quality per sample {% endcolumn %} {% endcolumns %} *** ## Population Summary **Population Summary card** features: * Link to the gnomAD variant entry for the specific dataset used for annotation. * Population statistics from a combined exome + genome gnomAD dataset: * **gnomAD All AF**: Overall alternative allele frequency across gnomAD populations. * **gnomAD Allele count**: Number of observed alternate alleles in the gnomAD dataset. * For mtDNA variants, **Homoplasmy Count** is shown instead. * **gnomAD Hom/Hemi count**: Number of gnomAD subjects who are homozygous or hemizygous for this variant. * For mtDNA variants, **Heteroplasmy Count** is shown instead. * **gnomAD Max AF**: The highest alternative allele frequency of the variant among gnomAD ancestry groups. For each ancestry group, Emedgene first combines gnomAD exome and genome counts, then takes the highest combined frequency: `(exome allele count + genome allele count) / (exome allele number + genome allele number)`. There is no minimum sample-size (AN) cutoff: a group is used even if it was genotyped in 1000 alleles or fewer.\ **Note:** Not to be confused with **Max AF (%)** in the **Variant table**, which is the highest frequency among all public population databases. In that column, gnomAD exomes and gnomAD genomes are compared separately, and an ancestry group is included only if AN > 1000. * **gnomAD Grpmax FAF (95% CI)** (v100.41+): The highest [filtering allele frequency](https://gnomad.broadinstitute.org/help/faf) observed across ancestry groups in a combined exome/genome gnomAD dataset. It uses a 95% confidence interval. * Available for SNV, indel, and MNV variants annotated with the [gnomAD 4.1 All](/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/gnomad-annotation-v100.41+.md) dataset. * Population statistics from organization databases, if available: * **Allele count**: Count of alternative alleles. * **Hom/Hemi count**: Count of alternative alleles in a homozygous or hemizygous state. The card is available for SNV/Indel, MNV (v100.39+), mtDNA SNV/Indel, DEL, DUP, INS, TRA (v100.41+), INV (v100.41+) variant types.

*** ### STR repeats distribution For STR variants, **STR Repeats Distribution** replaces the **Population Summary card**. It displays allele counts from gnomAD and 1000 Genomes, and gnomAD pathogenicity ranges.

*** ## Gene's related diseases The card features: * Number of gene–disease connections in the Emedgene knowledge base * Name of the selected disease * Inheritance mode(s) of the selected disease * GenCC validity badge (100.39+)\ When the selected disease has one or more GenCC (Gene Curation Coalition) database entries, a badge appears next to its inheritance mode. The badge represents the highest gene–disease validity classification.\ If multiple GenCC entries exist for the same gene–disease connection, a “+n” indicator appears beside the badge. Hover over the indicator to view additional classifications and their sources. * Links to the gene–disease connection source(s) for the selected disease: * OMIM * Academic papers in the Emedgene knowledge graph * CGD * ClinVar * Orphanet * GenCC (100.39+) {% hint style="info" %} **Note:** GenCC is included as a gene–disease source starting with [Emedgene knowledge base version 82](/emedgene/release-notes/knowledgebase_updates/2025/zoidberg-82-21st-october-2025.md). To view GenCC annotations in the UI, you must use [platform version 100.39](/emedgene/release-notes/workbench-and-pipeline-updates/new-in-emedgene-v100.39.0-october-16th-2025.md) or later. On older platform versions, the GenCC validity badge and submitter details are not displayed, and GenCC links are inactive. {% endhint %} * Link to the disease page in MONARCH (100.39+) * Phenotype match summary (displayed only for tagged variants): * Number of disease phenotypes that match the patient’s phenotypes, out of the total * List of disease phenotypes with indicated [match levels](/emedgene/emedgene-analyze-manual/reviewing_a_case/phenotypic-match/phenotypic_match_strength.md) {% hint style="warning" %} **TRA (v100.41+), INV (v100.41+), BND (v100.41+):** Gene-disease annotation for these variant types considers genes at the breakpoint position(s) where applicable. {% endhint %}

*** ## Pathogenicity View the user-assigned **Pathogenicity**. Change it or select a value from the dropdown when it is empty.

*** ## Clinical significance This card highlights existing pathogenicity classifications in public and private variant databases, including [**Curate**](/emedgene/emedgene-curate-manual/curate_variants.md). Each source has one badge. **Uncertain** and **Other** classifications appear only when that database has no **Benign/Likely Benign** or **Pathogenic/Likely Pathogenic** classifications for the variant. The card is available for SNV/Indel, MNV (v100.39+), mtDNA SNV/Indel, DEL, DUP, INS, TRA (v100.41+), INV (v100.41+), STR, haplotype variant types.

*** ## ACMG Classification Shows ACMG tags assigned to the variant and the resulting ACMG pathogenicity class and score. The card is available for SNV/Indel, mtDNA SNV/Indel, DEL, DUP variant types. **SNV/Indel, mtDNA SNV/Indel**

**ACMG Classification card** for sequence and mtDNA variants.

**DEL, DUP**

*** ## In Silico Prediction Overall estimates of *in silico* prediction results: **Missense Prediction**, **Conservation**, and **Splicing Prediction**. Availability of a specific prediction category depends on variant type: * **Small variant (SNV/Indel/MNV):** **Missense Prediction**, **Conservation**, and **Splicing Prediction** * **mtDNA (SNV/Indel):** **Missense Prediction, Conservation** * **Other variant types**: Not available

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