DOI: 10.5281/zenodo.17879697
title: GnomXMiss: Missense Variant Annotations Derived From AlphaMissense Enriched With gnomAD, VEP, and ClinVar

description: GnomXMiss per-protein files

<uniprot_id>_GnomXMiss.tsv

Each file contains available missense variants for a UniProt canonical protein present in the AlphaMissense data dump that could be crossed referenced with:





gnomAD allele frequencies (overall + subpopulation-specific)




AlphaMissense pathogenicity scores




VEP annotations (GENCODE v46)




ClinVar variant metadata



Only proteins for which all required annotations were successfully retrieved are included.

These files are sorted by residue_number and contain variants from the AlphaMissense hg38 missense dump together with variants in the matching genomic intervals of gnomad.joint.v4.1.sites.ht; we outer-merge both sources on (#CHROM, POS, REF, ALT) and annotate variants that lack information where possible.

Column descriptions

Below is the full set of columns that appear across the *_GnomXMiss.tsv files

Primary identifiers

uniprot_id

Canonical UniProtKB accession for the protein associated with the variant.

#CHROM

Chromosome name (e.g., chr1, chr2, chrX, chrY) based on GRCh38.

POS

1-based genomic coordinate of the variant (GRCh38).

REF, ALT

Reference and alternate nucleotides from gnomAD.

Protein-level variant information

protein_variant

Amino-acid substitution in the format <RefAA><Protein_Sequence_Position><AltAA>, e.g. V600E.

residue_number

Integer position of the substitution extracted from protein_variant.

AlphaMissense annotation

am_class

Classification of variant pathogenicity:





likely_benign




ambiguous




likely_pathogenic



am_pathogenicity

Calibrated AlphaMissense pathogenicity score (0–1).

ClinVar annotations (if available)

existing_variation

ClinVar or dbSNP IDs extracted via Ensembl VEP.

clinvar_significance

e.g., Benign, Likely_pathogenic, VUS, etc.

clinvar_condition

Name(s) of associated disease conditions.

clinvar_disease_id

Disease database identifiers (MEDGEN, MONDO, OMIM, etc.).

clinvar_variant_id

ClinVar Variation ID.

gnomAD allele frequency data (v4) (if available)

These fields are derived from the joint gnomAD v4 release and represent population-level statistics (no individual data).

Overall





allele_count




allele_number




allele_frequency




homozygote_count



Population-specific allele frequencies

The dataset includes AF values for multiple ancestry groups:





nfe_allele_frequency — Non-Finnish European




fin_allele_frequency — Finnish




afr_allele_frequency — African/African American




eas_allele_frequency — East Asian




sas_allele_frequency — South Asian




amr_allele_frequency — Latino/Admixed American




ami_allele_frequency — Amish




asj_allele_frequency — Ashkenazi Jewish




mid_allele_frequency — Middle Eastern




remaining_allele_frequency — Remaining ancestry group



Sex-specific allele frequencies





XX_allele_frequency




XY_allele_frequency



(Some fields be empty depending on variant representation in gnomAD.)
description: License

© 2025 Lucas Chataigner

This derived dataset is released under the Creative Commons Attribution 4.0 International License (CC-BY 4.0).You may obtain a copy of the license at:https://creativecommons.org/licenses/by/4.0

This dataset incorporates derived information from:





AlphaMissense (CC-BY-4.0, DeepMind Technologies Limited)




gnomAD v4 (CC-BY-4.0, Broad Institute / gnomAD Consortium)




ClinVar (Public Domain, NCBI/NLM/NIH)




Ensembl VEP (derivative-only annotations; VEP itself is GPLv3)




GENCODE v46 transcript models




UniProt identifiers (redistributable)



No raw upstream datasets are redistributed.All content is provided AS IS without warranty.