Variant info

The Variant info card provides key details about the variant.

Details included

• Variant type
• Main effect
• Cytoband
• Phasing (v100.40.0+, DRAGEN 4.5+, TruPath Genome data, SNVs/MNVs/indels):

  • Phase block identifier
  • Phased genotype (if available): A, B, AB
• Zygosity for each sequenced family member
• Gene symbol
• Transcript: Variant description in HGVS nomenclature, based on the selected transcript
• Exon information: Exon number and total number of exons for the selected transcript

Note: For some variants, exon information may be shown as -/-.

This is expected behavior when exon numbering is not applicable, such as for variants that span the entire transcript (for example, whole-gene or whole-transcript variants), intronic variants, or variants located outside the transcript.

• dbSNP ID (SNV/indel only)
• Resources: Links to external databases with pre-filled search queries
• CNV/SV-specific data:

  • SV type (e.g., DEL, DUP)
  • SV Length
  • DECIPHER link
  • ISCN notation

Variant badges

DRAGEN pipelines automatically assign variant badges to highlight specific call characteristics.

Integrating these badge filters into custom filter presets allows users to quickly identify variants that may need further review or validation. This streamlines interpretation and reduces manual sorting by grouping similar variants together.

Ambiguous Calling

• Labels potential de novo germline small variants in paralogous segmental duplication regions of the genome.
• Requires DRAGEN 4.3+ MRJD caller in High Sensitivity Mode (enabled by default when running DRAGEN through Emedgene).

Homology Region

• Labels small variants located in regions of high sequence similarity, reflecting potential mapping ambiguity due to paralogous sequences.
• Requires DRAGEN 4.3+ Small variant caller in High Sensitivity Mode (enabled by default when running DRAGEN through Emedgene).

Imprecise

• Labels structural variants for which the exact breakpoints could not be confidently determined.
• Requires DRAGEN v4.4+ Structural variant caller.

Potential Mosaic

• Labels potential mosaic small variants.
• Requires DRAGEN 4.3+ Small variant caller in Mosaic Detection Mode (enabled by default when running DRAGEN through Emedgene with an allele frequency threshold of 0.2).

Recombinant

• Identifies variants that may reflect recombination‑type sequence exchange between a gene and its highly similar pseudogene:

  • When the exchange is reciprocal, it can produce a gene deletion or duplication.
  • When the exchange is non‑reciprocal, it results in a gene conversion, where a segment of pseudogene sequence replaces the corresponding part of the functional gene.
• Applicable only to variants in the GBA1/GBAP1 and CYP21A2/CYP21A1P genes.
• Requires DRAGEN 4.3+ Targeted caller with the CYP21A2 and GBA callers enabled.

Repeat

Suspected MNP