---
title: Can I import my existing variant classifications into the VKB?
description: "Import variant classifications from Alissa, Congenica or another platform into the SeqOne VKB: files, required fields, class mapping, limits."
---

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# Can I import my existing variant classifications into the VKB?

## Learn how SeqOne imports the classifications and comments from your previous software into your Variant Knowledge Base (VKB).

Yes. SeqOne can import the variant classifications and comments from your previous interpretation software into your entity's Variant Knowledge Base (VKB). Once imported, each classification appears in the **VKB** column of every analysis in your entity that contains the variant.

Applies to: All worksets · Small variants (SNVs and indels) · GRCh37 and GRCh38 · Main and Preview · Spring 2026 (2.1)

The import is a service run by SeqOne, scoped and quoted for each project. You cannot start it yourself from the platform.

### What we can import

| Source | What you send | Variant types |
| --- | --- | --- |
| Alissa (Agilent) | Classification exports (MVL files) | SNVs and indels. CNVs are assessed case by case |
| Congenica | A classification export, on request, with the columns agreed with you | SNVs and indels. CNVs are assessed case by case |
| Another platform or an in-house database | A CSV or TSV file with the fields below | SNVs and indels. CNVs are assessed case by case |

### What your file needs

| Field | Required | Notes |
| --- | --- | --- |
| Variant | Yes | Chromosome, position, reference and alternate allele, or the HGVS c. notation with its transcript |
| Classification | Yes | One five-tier class per variant (see the mapping below) |
| Comment | No | Free text, for example your interpretation summary or the date of the classification |
| Genome build | Yes | GRCh37 or GRCh38, one build per file. Your VKB is tied to one genome build |

Important: Normalise (left-align) your indels before you send the file. An indel that is not normalised never matches a variant in your analyses.

### How your classes are mapped

| Class in your file | Class in the VKB |
| --- | --- |
| Pathogenic, 5 | Pathogenic |
| Likely pathogenic, 4 | Likely pathogenic |
| Uncertain significance, VUS, 3 | VUS |
| Likely benign, 2 | Likely benign |
| Benign, 1 | Benign |

Any other label, for example a class 0 or a local category, needs a mapping that you agree with us before the import.

### What you see after the import

- The **VKB** column of the Variant Viewer shows the imported class in every analysis of your entity that contains the variant.
- The imported comment appears under **Variant Description** in the **VKB Classification** tab of the **VKB Entry**.
- The **VKB History** tab shows the person who ran the import and the import date, not your original analyst.
- Deleting an analysis or a project does not remove the imported classifications.

### Limitations

As of Spring 2026 (2.1):

- Only the latest classification of each variant is imported, not its history.
- The original analyst and classification date are not kept as VKB fields. For Alissa imports, the original date is added at the start of the comment.
- Imported classifications are not linked to samples, so they do not add to sample frequency or occurrences.
- If a variant is already in your VKB, its existing classification is kept unless you ask us to overwrite it.
- If your file holds the same variant several times, you choose the rule: the most recent or the most pathogenic classification.
- Imported variants may not appear in the VKB search until they are evaluated in a SeqOne analysis.

### How to request an import

1. Contact the SeqOne Support team or your account manager. Tell us your source software, the variant types, the genome build and the approximate number of variants.
2. We confirm what can be imported and send you a quote.
3. Send your export file, with your class mapping and your rule for duplicates.
4. We import the file and send you an import summary: variants imported, skipped and rejected.
5. Check a sample of the imported variants in your analyses, then confirm the import.

Tip: Import your classifications before you validate SeqOne on your own samples. Your validation analyses then show your existing VKB.

To learn how the VKB works, read [Intro to the VKB V2](https://support.seqone.com/knowledge-base/intro-to-the-vkb-v2?hsLang=en).

**Still need help?** Contact our Support team at [support@seqone.com](mailto:support@seqone.com).

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