Transcript

The Transcript field displays variant description according to the Human Genome Variation Society (HGVS) standard for coding DNA and protein changes.

Some transcripts are marked with one or both indicators:

• Checkmark : Canonical transcript

• Curate icon: Transcript selected in your Curate database.

Emedgene automatically selects a reference transcript according to predefined prioritization rules. The reference transcript determines:

• Main affected gene

• Main variant effect

• Coding DNA change and resulting protein change

Changing the reference transcript

If the automatically selected transcript does not match your reporting preference, you can:

• Select a different transcript* from the Transcript dropdown menu

• Add a custom transcript as part of a custom HGVS variant description (see below). You may need to add a custom HGVS variant description in the following cases:

  • The required transcript is not available in the suggested options

  • Certain variants, such as upstream or downstream gene variants, may be lacking an automatic HGVS description

*Transcript selection restriction to maintain variant-gene consistency

When a variant occurs in a region shared by transcripts from different genes, Emedgene enforces a rule:

You cannot select a transcript that belongs to a different gene than the variant's primary gene.

This restriction prevents mismatches between the variant and its gene context, which could lead to incorrect interpretation. If you try to select a transcript from a non-primary gene, the option is blocked.

How to add a custom HGVS variant description

1

Click the plus icon next to the HGVS description box.

2

In the field, enter the notation in the correct format. Do not include spaces.

• Coding change only: GENE,NM_123456:c.-123A>C

• Coding and protein change: GENE,NM_123456:c.123G>A,p.123Arg>His

Once added, a custom description becomes available for reporting.