4624f2c72c429fd9b32532bb4d9b62f030b50182 max Wed Sep 9 06:00:44 2026 -0700 trackDb: cross-link the Deleteriousness Predictions container with the CADD 1.6, CADD 1.7, REVEL and AlphaMissense tracks on hg38 and hg19, refs #38261 diff --git src/hg/makeDb/trackDb/relatedTracks.ra src/hg/makeDb/trackDb/relatedTracks.ra index 97cea089e65..ca64c983d8d 100644 --- src/hg/makeDb/trackDb/relatedTracks.ra +++ src/hg/makeDb/trackDb/relatedTracks.ra @@ -561,72 +561,88 @@ hg38 gwasCatalog gtexEqtlHighConf Variants that change gene expression, often used to find the gene behind an association signal hg38 gtexEqtlHighConf gwasCatalog Trait and disease association signals these expression effects are usually compared against hg38 snpedia varsInPubs Individual variants mentioned in the literature, text-mined from full-text papers hg38 varsInPubs snpedia Wiki summaries of what has been published about individual SNPs hg19 gwasCatalog varsInPubs Individual variants mentioned in the literature, text-mined from full-text papers hg19 varsInPubs gwasCatalog Trait and disease associations from published genome-wide association studies hg19 gwasCatalog snpedia Wiki summaries of what has been published about individual SNPs hg19 snpedia gwasCatalog The underlying published associations, with effect sizes and p-values hg19 snpedia varsInPubs Individual variants mentioned in the literature, text-mined from full-text papers hg19 varsInPubs snpedia Wiki summaries of what has been published about individual SNPs # Variant impact predictor cross-links: hg38 mutScore primateAi A pathogenicity predictor that also works from 3D protein structure hg38 primateAi mutScore Missense variant clustering within 3D protein structures -hg38 mutScore revel An ensemble missense pathogenicity score built from multiple predictors +hg38 mutScore revel An ensemble missense pathogenicity score, recommended by the ACMG, built from multiple predictors hg38 revel mutScore Missense variant clustering within 3D protein structures hg38 mutScore alphaMissense A deep-learning missense pathogenicity predictor hg38 alphaMissense mutScore Missense variant clustering within 3D protein structures hg38 mutScore clinPred An ensemble missense pathogenicity predictor that incorporates gnomAD allele frequency hg38 clinPred mutScore Missense variant clustering within 3D protein structures hg38 >caddSuper1_7 revel An ensemble pathogenicity score for coding variants hg38 >caddSuper1_7 clinPred An ensemble missense pathogenicity predictor that incorporates gnomAD allele frequency hg38 >caddSuper1_7 alphaMissense A deep-learning missense pathogenicity predictor hg38 >caddSuper1_7 gnomadVariants Population allele frequencies, useful for judging whether a high-scoring variant is common +hg38 predictionScoresSuper caddSuper1_7 A deleteriousness score for all single-base substitutions and selected indels, coding and non-coding +hg38 caddSuper1_7 predictionScoresSuper Other variant impact and pathogenicity prediction scores +hg38 predictionScoresSuper caddSuper The previous CADD release, with the older model and training set +hg38 caddSuper predictionScoresSuper Other variant impact and pathogenicity prediction scores +hg38 predictionScoresSuper revel An ensemble missense pathogenicity score for coding variants +hg38 revel predictionScoresSuper Other variant impact and pathogenicity prediction scores +hg38 predictionScoresSuper alphaMissense A deep-learning missense pathogenicity predictor +hg38 alphaMissense predictionScoresSuper Other variant impact and pathogenicity prediction scores hg19 >caddSuper1_7 gnomadSuper Population allele frequencies, useful for judging whether a high-scoring variant is common hg19 mutScore primateAi A pathogenicity predictor that also works from 3D protein structure hg19 primateAi mutScore Missense variant clustering within 3D protein structures hg19 mutScore revel An ensemble missense pathogenicity score built from multiple predictors hg19 revel mutScore Missense variant clustering within 3D protein structures hg19 mutScore alphaMissense A deep-learning missense pathogenicity predictor hg19 alphaMissense mutScore Missense variant clustering within 3D protein structures hg19 mutScore clinPred An ensemble missense pathogenicity predictor that incorporates gnomAD allele frequency hg19 clinPred mutScore Missense variant clustering within 3D protein structures hg19 >caddSuper1_7 revel An ensemble pathogenicity score for coding variants hg19 >caddSuper1_7 clinPred An ensemble missense pathogenicity predictor that incorporates gnomAD allele frequency hg19 >caddSuper1_7 alphaMissense A deep-learning missense pathogenicity predictor +hg19 predictionScoresSuper caddSuper1_7 A deleteriousness score for all single-base substitutions and selected indels, coding and non-coding +hg19 caddSuper1_7 predictionScoresSuper Other variant impact and pathogenicity prediction scores +hg19 predictionScoresSuper caddSuper The previous CADD release, with the older model and training set +hg19 caddSuper predictionScoresSuper Other variant impact and pathogenicity prediction scores +hg19 predictionScoresSuper revel An ensemble missense pathogenicity score for coding variants +hg19 revel predictionScoresSuper Other variant impact and pathogenicity prediction scores +hg19 predictionScoresSuper alphaMissense A deep-learning missense pathogenicity predictor +hg19 alphaMissense predictionScoresSuper Other variant impact and pathogenicity prediction scores # Splicing impact cross-links: hg38 ~spliceAI abSplice Another deep-learning predictor of splice-altering variants hg38 spliceAI spliceVarDb Splicing variants with experimental validation, useful for checking these predictions hg38 spliceVarDb spliceAI Predicted splice-altering effects, scored genome-wide hg38 spliceAI spliceAIWt The same model run on the reference sequence, showing where splicing is expected without any variant hg38 spliceAIWt spliceAI The same model scored for variants, rather than for the reference sequence hg38 abSplice spliceVarDb Splicing variants with experimental validation, useful for checking these predictions hg38 spliceVarDb abSplice Predicted aberrant splicing, scored per variant and tissue hg38 spliceImpactSuper predictionScoresSuper Pathogenicity scores for coding and non-coding variants generally, not only splicing hg38 predictionScoresSuper spliceImpactSuper Prediction scores and databases for variants that disrupt splicing hg38 nmd spliceImpactSuper Predicted and validated splice-altering variants, a common source of premature termination codons hg38 spliceImpactSuper nmd Regions where premature termination codons are predicted to escape nonsense-mediated decay hg19 ~spliceAI abSplice Another deep-learning predictor of splice-altering variants hg19 spliceImpactSuper predictionScoresSuper Pathogenicity scores for coding and non-coding variants generally, not only splicing hg19 predictionScoresSuper spliceImpactSuper Prediction scores and databases for variants that disrupt splicing # Constraint score cross-links: hg38 constraintSuper predictionScoresSuper Per-variant deleteriousness and pathogenicity scores, rather than regional constraint hg38 predictionScoresSuper constraintSuper Regional and gene-level constraint measured from population variation hg38 ~jarvis ukbDepletion Another score for how depleted of variation a non-coding region is hg38 ~hmc gnomadPLI Another constraint metric derived from the absence of variation in population data -hg38 hmc ucscGenePfam The Pfam domains that homologous missense constraint is calculated over +hg38 hmc ucscGenePfam The Pfam protein domains that homologous missense constraint is calculated over hg38 ucscGenePfam hmc Missense constraint measured across homologous positions within these domains hg38 promoterAi jarvis A score prioritizing non-coding regions more broadly, not only promoters hg38 jarvis promoterAi A deep-learning predictor for variants in promoter regions specifically hg19 constraintSuper predictionScoresSuper Per-variant deleteriousness and pathogenicity scores, rather than regional constraint hg19 predictionScoresSuper constraintSuper Regional and gene-level constraint measured from population variation hg19 ~jarvis ukbDepletion Another score for how depleted of variation a non-coding region is hg19 ~hmc gnomadPLI Another constraint metric derived from the absence of variation in population data hg19 hmc ucscGenePfam The Pfam domains that homologous missense constraint is calculated over hg19 ucscGenePfam hmc Missense constraint measured across homologous positions within these domains