GeneBe

Genetic Variant Interpretation Tool

GeneBe is a portal that helps with genetic variant interpretation. It aggregates variant data from multiple sources, allowing you to check variant function, GnomAD frequencies, and ClinVar annotations, and use our ACMG variant pathogenicity calculator.

Use the search box to find annotations for specific genetic variants or genes.

Examples:

Other things that GeneBe can do

GeneBe is not only a website or an ACMG score calculator.
  • Check our API with a dedicated Python client that can annotate variants in Python Pandas dataframe. If you need to annotate your VCF files with ACMG scores, population frequencies etc. you can use our genebe-cli tool.
  • Check our tool for liftover variants between hg19/hg38/t2t in batches.
  • And another tool for converting HGVS variant notations to positions in batches.

Find out more about GeneBe on our about page.

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News & Changelog

  1. New Java Client for VCF Annotation

    We're incubating a new Java client for annotating VCF files, available at genebe-cli. While still in alpha, it’s recommended over the Python client for VCF annotation. Read more here.

  2. ClinGen Evidence Repository Pathogenicity Assignments

    We are now incorporating pathogenicity assignments from the ClinGen Evidence Repository where possible, showing ClinGen verdict instead of automatically assigned ACMG verdict. Learn more about the ClinGen repository here.

  3. GnomAD 4.1 and Ensembl VEP Plugin Integration

    Our latest update now utilizes GnomAD v. 4.1, further expanding our dataset. Additionally, we have integrated the GeneBe plugin into Ensembl VEP. Learn more about the plugin here.

  4. GnomAD4, CADD 1.7 and Minor Updates

    We have updated our algorithm to use GnomAD v. 4.0 (over 800,000 individuals!) and CADD 1.7 in the score assignment. Give it a try.

  5. Exciting News: GeneBe in Clinical Genetics!

    We're thrilled to announce the publication of our latest article, Genebe.net: Implementation and Validation of an Automatic ACMG Variant Pathogenicity Criteria Assignment in Clinical Genetics.

  6. New Introduction Article

    A short introduction on using the GeneBe REST API via the Python library was published on Medium: Annotating Genetic Variants Made Easy.

  7. The Python client becomes open source.

    GeneBe's Python client is now open source. Check it out on GitHub, along with the documentation.

  8. GnomAD4 and Python Client

    We have updated our GnomAD database to use version 4. Although it is not yet utilized in the ACMG algorithm, the data is displayed on the website.

    There is a new experimental GeneBe Python Client available on PyPI.

  9. Welcome to new scorers: AlphaMissense and CardioBoost; API is production ready.

    The API for annotating variants is ready. It offers speed (processing over 500 variants per second for WGS), completeness (covering ACMG guidelines, frequencies, scores, and consequences), and reliability. Create an account and generate an API key to use API.

    Additionally, we have integrated AlphaMissense and CardioBoost scores on the page.

  10. Presentation at PTGC 2023

    Presentation 'Genebe.net – automatic implementation of ACMG criteria' delivered at the 11th Congress of the Polish Society of Human Genetics, Bydgoszcz, Poland.