Manually add variants to a delivered case

In some cases, you may need to record variants that were not included in the uploaded VCF or not called from FASTQ data. This is particularly useful when:

• You are complementing NGS results with findings from other genetic tests (e.g., long-read sequencing, optical mapping, CGH, SNP array, karyotyping/FISH, repeat-primed PCR, MLPA, Southern blot, etc.)

• You wish to report on adjacent CNV calls as a single CNV event.

• You wish to report a set of adjacent variants together as a single multi-nucleotide variant (MNV).

Manually adding variants ensures that all relevant findings are visible in the case review and can be considered during interpretation.

Currently supported variant types: SNV, CNV, UPD, ROH, and STR.

To manually add a variant:

1. Open the Analysis Tools tab.

2. Click the plus (+) button in the top-right corner.

1. In the Manually Add Variant window, select the variant type: SNV, CNV, UPD, ROH, or STR.

2. Fill in the details based on the selected type:

SNV or ROH

CNV or UPD

STR

• Chromosome,

• Position,

• REF,

• ALT,

• Zygosity

• Chromosome,

• Position Start,

• Position End,

• REF,

• ALT,

• Type:

  • CNV: DEL, DUP,

  • UPD: IUPDMAT (maternal isodisomy), IUPDPAT (paternal isodisomy), HUPDPAT (paternal heterodisomy), HUPDMAT (maternal heterodisomy),

• Zygosity

• Chromosome,

• Position,

• REF Repeats Number,

• ALT Repeats Number,

• Repeats Unit,

• Zygosity

1. Click on Create Variant to add it to the case.

Viewing manually added variants

• Manually added variants have a blue frame and are clearly marked with the label “Manually added variant” on the Variant page.

• These variants differ from pipeline-called variants:

  • Quality and Visualization sections are not available.

  • Population Statistics are not shown.

  • Automatic ACMG scoring is not applied, but you can still manually add ACMG tags, interpretation notes, and classifications.

Sorting and formatting notes

• STR variants that are added manually do not fully align with the pipeline-called STR format. For example, variant length is not displayed.

• Manually added variants cannot be sorted by columns that do not apply, such as AI Rank.

Filtering manually added variants

To view only the variants you have added manually:

• In the Evidence & Tags Filters section, select Manually added variants.

This helps you focus specifically on variants that were entered outside of the automated pipeline.