Downloading variant annotation data

When an analysis in VarSome Clinical has finished, there are several ways you may download annotated variants.

Annotated variants in Excel format

You can download up to 50000 variants from the variant table in Excel format by clicking on the downloads icon.

Filtered annotated variants in Excel format

If you wish to download only the filtered variants in an excel sheet with all annotation data click on the icon available above the variant table after having filtered your results table using the dynamic filters.

Annotated VCF file

You can download the annotated VCF file by going to the "Downloads" option in the drop-down menu of the "Analysis Actions".

The downloaded VCF will contain the following annotation data in the 8th column named "INFO":

• AC = Allele count in genotypes for the alternative allele 
• ACMG attributes:
  • ACMG_class = Benign, Likely Benign, Uncertain Significance, Likely Pathogenic, Pathogenic”
  • ACMG coding impact
  • ACMG_gene
  • 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

• ClinVar classifications
• pathogenicity scores
• AF = Allele frequency for the alternative allele
• AN = Total number of alleles in called genotypes
• BaseQRankSum = Rank sum test of REF versus ALT base quality scores
• ClippingRankSum = Rank sum test for hard-clipped bases on REF versus ALT reads
• ExcessHet = Phred-scaled p-value for exact test of excess heterozygosity
• CGD inheritance 
• FS = Phred-scaled p-value using Fisher's exact test to detect strand bias
• Gene linked to the variant
• MLEAC = Maximum likelihood expectation (MLE) for the allele counts, for each ALT allele
• MLEAF = Maximum likelihood expectation (MLE) for the allele frequency, for each ALT allele
• MQ = Mapping quality
• MQRankSum = Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities
• QD = Variant Confidence/Quality by Depth
• ReadPosRankSum = Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias
• function = Variant function within a transcript containing this variant
• allele frequencies from GnomAD (gnomadGenomesAC, gnomadGenomesAN, gnomadGenomes_AC_Hom, gnomadGenomes_AF)
• all the transcripts for the given gene from Ensembl and RefSeq

(an explanation for the annotations is given within the file)

The downloaded VCF will also contain the following annotation data:

• AMP attributes:
  • AMP_matches = Cancer & tissue type matches for this sample
  • AMP_rules = Rules & tiers triggered in the AMP classification
  • AMP_score = Pathogenicity score: from 0 = Benign to >3 = Tier I
  • AMP_tier = AMP Tier I, II, III or IV
  • AMP_total_samples = Total count of samples across somatic databases
• DANN_score
• MutationTaster_pred = Mutation taster prediction
• MutationTaster_score = Mutation taster Score
• cosmicFathMMPrediction = FathMMP prediction from COSMIC
• cosmicFathMMScore,Number=1,Type=Float,Description="FathMMP score from COSMIC">

Download only selected variants

You can also select a specific subset of variants to generate a clinical report (find here more information about this feature).

After having selected the variants of interest, click on the icon:  and then a pop-up window will appear that will redirect you to VarSome Clinical's clinical report generation page, by clicking on the icon.