---
title: What is the ComPerMed classification?
description: Learn how to interpret the ComPerMed classification of somatic variants.
---
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# What is the ComPerMed classification?
## Learn how to interpret the ComPerMed classification of somatic variants.
The ComPerMed classification is a two-level workflow system established by a panel of Belgian experts to **standardize the classification of somatic variants** detected in solid and haematological tumours by Next-Generation Sequencing (NGS). The overarching goal is to achieve high consistency in diagnosis, prognosis, treatment, and follow-up of cancer patients across different laboratories.
The ComPerMed classification is assigned in SeqOne through an automated, computational process. Users can click the ComPerMed score of any variant to open the variant page and review the criteria used for class assignment, as well as the variant's presence in several databases.
The [ComPerMed publication](https://pmc.ncbi.nlm.nih.gov/articles/PMC6966529/) describes the precise class assignment workflow; below are presented the main elements:
The main elements of the classification workflow are:
- **Consensus Pathogenic Variant (CPV) List:** The variants are checked against a CPV list established by ComPerMed experts for clinically relevant driver mutations (hotspots) in selected genes for solid and myeloid tumours. Variants present in the CPV list are classified as Pathogenic.
- **Loss-of-Function (LoF) Variant Assessment:** Variants not on the CPV list are assessed based on their predicted functional impact. Clear LoF variants (frameshift, nonsense, AG/GT splice site variants) in tumour suppressor (Ts) genes are classified as Likely Pathogenic. Clear LoF variants in oncogenes are classified as VUS.
- **Scoring Table for Non-LoF Variants:** Missense variants and in-frame indels in Ts- or oncogenes are evaluated using a scoring table with four parameters:
- Total number of entries in COSMIC.
- Presence in lists of Ts- and oncogenes (OncoKb, TSGene 2.0, Vogelstein et al., IntOGen).
- Report of tumorigenicity in functional studies (PubMed, Jax-CBK, MD Anderson PCT, My Cancer Genome).
- Presence as (Likely) Pathogenic in databases (CIVIC, ClinVar, OncoKb, VarSome) in a somatic context.
A total score of ≥2 results in a Likely Pathogenic classification, while a score of \<2 results in VUS. For variants in genes not on the CPV list, a maximal score of +3.5 can lead to a Pathogenic classification.
- **Population Database Check:** Variants are checked against healthy population databases (gnomAD), and assigned as Benign or Likely Benign depending on their frequency.
In summary, the ComPerMed classification provides a structured and harmonized approach to first determine the biological relevance of somatic variants and then interpret their clinical significance in the context of cancer.
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