Score datasources

caution

This page is for development only and not part of the public documentation.

Name	Full Name	Link	Comment
BayesDel_addAF	BayesDel with allele frequency	link	Bayesian framework using allele frequencies for variant prediction
BayesDel_noAF	BayesDel without allele frequency	link	Variant effect score without allele frequency input
CADD	Combined Annotation Dependent Depletion	link	Integrates multiple annotations into a single deleteriousness score; freely available only for non-commercial use
DANN	Deleterious Annotation of genetic variants using Neural Networks	link	Deep neural network-based pathogenicity score
Eigen	Eigen score	link	Unsupervised learning on functional annotations
Eigen_PC	Eigen score with principal components	link	PCA-normalized version of Eigen
FATHMM_MKL	Functional Analysis through Hidden Markov Models	link	Uses multiple kernel learning on functional data
MetaRNN	Meta Recurrent Neural Network	link	RNN-based ensemble method for variant classification
MetaSVM	Meta Support Vector Machine	link	Ensemble score using SVM on functional features
PrimateAI	PrimateAI	link	Deep learning score using primate sequences to model constraint
PROVEAN	Protein Variation Effect Analyzer	link	Measures functional impact of protein sequence variation
REVEL	Rare Exome Variant Ensemble Learner	link	Ensemble method optimized for rare missense variants
Sift	Sorting Intolerant From Tolerant	link	Predicts whether amino acid changes affect protein function
Sift4G	SIFT 4 Genomes	link	Faster and more scalable version of SIFT
Vest4	Variant Effect Scoring Tool 4	link	Machine learning-based variant impact predictor
ClinPred	Clinical Prediction of variant pathogenicity	link	Classifies variants using clinical features
GERP RS	Genomic Evolutionary Rate Profiling RS	link	Measures evolutionary conservation of genomic positions
gMVP	Genomic Mutation Vulnerability Predictor	link	Neural network trained on ClinVar and gnomAD annotations

Name	Full Name	Link	Comment
ADA	Adaptive Boosting Splice Site Score	link	Uses ensemble learning (AdaBoost) to predict splice-altering variants
RF	Random Forest Splice Site Score	link	Random forest classifier trained to predict splicing disruption
SpliceAI	Splicing Artificial Intelligence	link	Deep neural network predicting splicing from raw sequence