When an analysis in VarSome Clinical has finished, there are several ways you may download annotated variants.
Annotated VCF file
You may download the annotated VCF file by selecting the option in the drop-down menu of the "Analysis Actions". You will get the following annotation data:
- allele frequencies from GnomAD
- ACMG_class = Benign, Likely Benign, Uncertain Significance, Likely Pathogenic, Pathogenic”
- ACMG_gene = HGNC gene symbol of the gene used for the ACMG annotation
- ACMG_rules = Rules & strengths triggered in the ACMG classification
- ACMG_score = Pathogenicity score: from 1 = Benign to >=5 = Pathogenic, use this to sort by pathogenicity, particularly useful for uncertain variants with weak clinical evidence.
- ACMG_transcript = Transcript used by the ACMG annotation
- CGD inheritance
- gene linked to the variant
- all the transcripts for the given gene
- variant function
- ClinVar classifications
- pathogenicity scores
Filtered variants in Excel
If you wish to download only the filtered variants in an excel sheet with all annotation data click on the "Filtered Variants" button (next to "Analysis Actions").
Download only selected variants
Also, you may download an excel sheet with only selected variants.