Emedgene
Illumina Connected Software
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      • Clinical Significance section
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      • CNV overlap percentage
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      • ACMG SNV Classification wizard
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      • ACMG CNV Classification wizard
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  • Frequently Asked Questions
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      • Which browser should I use with Emedgene?
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      • How do I prepare VCF files generated by DRAGEN MANTA to be used as input for Emedgene?
      • Source of gnomAD data for small variants on GRCh38
      • How are MNVs handled on the platform?
      • Support for gene lists with up to 10,000 genes
      • Genomic Regions by Case Type
      • How do I analyze mtDNA variants?
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      • How does joint calling work on Emedgene?
      • What is the required format for a BED file defining a kit?
      • Which reference genomes can I use?
      • How do I move between organizations?
      • How do I check the version of my environment?
      • "Failed to generate report". What should I do?
      • How do I prepare VCF files generated by Dragen STR (ExpansionHunter) to be used as input?
      • How does Emedgene Analyze prioritize transcripts?
      • How does Emedgene Analyze merge variants from different sources?
      • Performance issue troubleshooting
      • How does Emedgene calculate variant effect and severity ?
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  • Release Notes
    • Workbench & Pipeline Updates
      • New in Emedgene V37.0 (February 20, 2025)
        • V37 Patches
      • New in Emedgene V36.0 (October 8 2024)
        • V36 Patches
      • New in Emedgene V35.0 (May 22nd 2024)
        • V35 Patches
      • New in Emedgene V34.0 (January 28th 2024)
        • V34 Patches
      • New in Emedgene V33.0 (September 6th 2023)
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      • New in Emedgene V32.0 (June 8th 2023)
        • New pipeline 32 (June 8th 2023)
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      • More release notes
        • New in emedgene 31 (March 1st 2023)
        • New in emedgene 30 (January 8th 2023)
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        • New pipeline 5.29 (May 1st 2022)
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      • 2025
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      • 2024
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      • 2023
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  • Where can I review and edit the ACMG Classification of a CNV?
  • How do I review and edit the ACMG Classification of a CNV?
  • The ACMG CNV Classification wizard features:

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  1. Emedgene analyze manual
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ACMG CNV Classification wizard

PreviousLogic behind ACMG classification of SNVsNextVariant page sidebar (2.29+)

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Where can I review and edit the ACMG Classification of a CNV?

The ACMG CNV Classification wizard is located in the of the . Itis available for tagged genomic variants.

The tool automatically scores sections 1, 2, 3, and partially scores sections 4 and 5 of the , including the full PVS1 calculation required for intragenic variants. All the relevant data is summarized in an accessible table.


How do I review and edit the ACMG Classification of a CNV?

The ACMG CNV Classification wizard features:

  1. Automatically calculated ACMG class | ACMG score

  1. ACMG score sliderdepicting ranges of ACMG score values for each ACMG class and where the current classification falls: Benign: ≤-0.99; Likely Benign: -0.98...-0.90; VUS: -0.89...0.89; Likely Pathogenic: 0.90...0.98; Pathogenic: ≥0.99.

  1. Reclassify button that enables Edit mode

  1. Gene Number:

    • Number of protein-coding RefSeq genes overlapped by the CNV; of these:

  2. Genes affected by breakpoints - protein-coding RefSeq genes affected by CNV's breakpoints, and positions of breakpoints relative to the canonical transcript of each affected gene. Keep in mind that sometimes a breakpoint falls into more than one gene because genes may overlap.

  1. Gene table that provides a summary of the affected protein-coding genes:

    • Gene description:

      • Name - HGNC gene symbol,

      • Strand orientation;

    • Overlap info:

      • Gene - percentage of a gene involved in a CNV,

      • CNV - percentage of a CNV that overlaps with a gene;

    • ClinGen dosage sensitivity scores:

      • TS - ClinGen triplosensitivity score,

      • HI - ClinGen haploinsufficiency score;

    • HI predictors:

      • gnomAD pLI score (colored in red if pLI > 0.9),

      • DECIPHER HI index (colored in red if HI < 10);

    • Canonical transcript:

      • RefSeq ID,

      • 5’ UTR - affected or not,

      • CDS:

        • exons involved out of total,

        • NMD flag if the CNV is predicted to undergo nonsense mediated decay.

        • ClinVar flag if there are Clinvar Path SNV in the last exon

c. With the _Edit tag_ option, users can modify a particular criterion: 1. select a different criterion within a section, 2. add notes, 3. change the criterion's score [where applicable\*](acmg_cnv_classification_wizard.md#h_6cd626ed23).

```
d. You may choose to review and adjust evidence section-by-section using the _Reclassify_ option.

*Criteria with variable score:

  • 2F, 2I;

  • 4A, 4B, 4C, 4D, 4E, 4I, 4J, 4K, 4L, 4M, 4N, 4O;

  • 5A, 5B, 5C, 5E, 5G, 5H.

This tool is highly accurate and can save 75-90% of manual review time for CNVs ().

Number of established ClinGen genes, i.e., genes with sufficient evidence of dosage sensitivity (defined by having of 3) or dosage insensitivity (scores of 40),

Number of predicted haploinsufficient genes (if applicable) - defined as genes with gnomAD probability of loss of function intolerance (pLI) score ≥0.9 and the DECIPHER HI index ≤10.00.

3’ UTR - affected or not.

Evidence sections. The wizard is designed to allow users to easily edit and rescore each section: a. In each section, the criterion selected is color-coded based on its score (hence, pathogenicity of the piece of evidence): * green indicates negative scores (benign evidence), * grey indicates zero (neutral evidence), and * red indicates positive scores (pathogenic evidence).

b. Clicking on a section box reveals the active criterion, its score, and notes box. Here you can: i. add notes; ii. change the criterion's score .

```

```

ASHG 2020 abstract
ClinGen's Haploinsufficiency and/or Triplosensitivity scores
where applicable*
Evidence section
Variant page
ACMG/Clingen guidelines