Manually add variants to a delivered case

When you:

• Complement NGS with other genetic tests done on the side (long-read sequencing, optical mapping, CGH, SNP array, karyotyping/FISH, repeat-primed PCR, MLPA, Southern blot, etc), or

• Choose to report a few adjacent variants as a single multi-nucleotide variant,

the need to add variants on top of the analysis results arises.

You can manually add variants absent from the VCF or not called from the FASTQ. Supported variant types are SNV, CNV, UPD, ROH, and STR. SV is coming soon!

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To manually add a variant:

1. Click on the plus button on the top right of the Analysis tools tab.

Note: if you do not see this option, please contact us and we will provide you with the relevant user role.

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

2. Fill in variant details according to the selected variant type:

SNV or ROH

• Chromosome,

• Position,

• REF,

• ALT,

• Zygosity

CNV or UPD

• 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

STR

• Chromosome,

• Position,

• REF Repeats Number,

• ALT Repeats Number,

• Repeats Unit,

• Zygosity

1. Click on Create Variant.

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Manually added variant's Variant page

Unlike regular variants, the manually added variant's Variant page has a blue frame and a "Manually added variant" title.

Note: Quality and Visualization sections of the Variant page are not relevant for manually added variants, and Population Statistics section is not available for now. Automatic assignment of ACMG criteria is not available for manually added variants but you may manually select the relevant tags and the final variant class will be calculated on the fly.

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To filter by manually added variants:

In User filters select Manually added variants: