CADD
In the GTB format CADD database, 119 annotation fields from CADD v1.7 have been selected and organized into 8 categories: Chromatin States (25 fields), Conservation (15 fields), Epigenetics (28 fields), Mutability (11 fields), Protein Function (22 fields), Proximity Table (4 fields), RegSeq (9 fields), and Transcription Factors (5 fields).
| Category | Field | Description | Type |
|---|---|---|---|
| ChromatinStates | chmm_e1 | Number of 48 cell types in chromHMM state E1_poised (default: 1.92) | Float |
| ChromatinStates | chmm_e2 | Number of 48 cell types in chromHMM state E2_repressed (default: 1.92) | Float |
| ChromatinStates | chmm_e3 | Number of 48 cell types in chromHMM state E3_dead (default: 1.92) | Float |
| ChromatinStates | chmm_e4 | Number of 48 cell types in chromHMM state E4_dead (default: 1.92) | Float |
| ChromatinStates | chmm_e5 | Number of 48 cell types in chromHMM state E5_repressed (default: 1.92) | Float |
| ChromatinStates | chmm_e6 | Number of 48 cell types in chromHMM state E6_repressed (default: 1.92) | Float |
| ChromatinStates | chmm_e7 | Number of 48 cell types in chromHMM state E7_weak (default: 1.92) | Float |
| ChromatinStates | chmm_e8 | Number of 48 cell types in chromHMM state E8_gene (default: 1.92) | Float |
| ChromatinStates | chmm_e9 | Number of 48 cell types in chromHMM state E9_gene (default: 1.92) | Float |
| ChromatinStates | chmm_e10 | Number of 48 cell types in chromHMM state E10_gene (default: 1.92) | Float |
| ChromatinStates | chmm_e11 | Number of 48 cell types in chromHMM state E11_gene (default: 1.92) | Float |
| ChromatinStates | chmm_e12 | Number of 48 cell types in chromHMM state E12_distal (default: 1.92) | Float |
| ChromatinStates | chmm_e13 | Number of 48 cell types in chromHMM state E13_distal (default: 1.92) | Float |
| ChromatinStates | chmm_e14 | Number of 48 cell types in chromHMM state E14_distal (default: 1.92) | Float |
| ChromatinStates | chmm_e15 | Number of 48 cell types in chromHMM state E15_weak (default: 1.92) | Float |
| ChromatinStates | chmm_e16 | Number of 48 cell types in chromHMM state E16_tss (default: 1.92) | Float |
| ChromatinStates | chmm_e17 | Number of 48 cell types in chromHMM state E17_proximal (default: 1.92) | Float |
| ChromatinStates | chmm_e18 | Number of 48 cell types in chromHMM state E18_proximal (default: 1.92) | Float |
| ChromatinStates | chmm_e19 | Number of 48 cell types in chromHMM state E19_tss (default: 1.92) | Float |
| ChromatinStates | chmm_e20 | Number of 48 cell types in chromHMM state E20_poised (default: 1.92) | Float |
| ChromatinStates | chmm_e21 | Number of 48 cell types in chromHMM state E21_dead (default: 1.92) | Float |
| ChromatinStates | chmm_e22 | Number of 48 cell types in chromHMM state E22_repressed (default:1.92) | Float |
| ChromatinStates | chmm_e23 | Number of 48 cell types in chromHMM state E23_weak (default: 1.92) | Float |
| ChromatinStates | chmm_e24 | Number of 48 cell types in chromHMM state E24_distal (default: 1.92) | Float |
| ChromatinStates | chmm_e25 | Number of 48 cell types in chromHMM state E25_distal (default: 1.92) | Float |
| Conservation | priPhCons | Primate PhastCons conservation score (excl. human) (default: 0.0) | Float |
| Conservation | mamPhCons | Mammalian PhastCons conservation score (excl. human) (default: 0.0) | Float |
| Conservation | verPhCons | Vertebrate PhastCons conservation score (excl. human) (default: 0.0) | Float |
| Conservation | priPhyloP | Primate PhyloP score (excl. human) (default: -0.029) | Float |
| Conservation | mamPhyloP | Mammalian PhyloP score (excl. human) (default: -0.005) | Float |
| Conservation | verPhyloP | Vertebrate PhyloP (excl. human) (default: 0.042) | Float |
| Conservation | GerpN | Neutral evolution score defined by GERP++ (default: 3.0) | Float |
| Conservation | GerpS | Rejected Substitution score defined by GERP++ (default: -0.2) | Float |
| Conservation | GerpRS | Gerp element score (default: 0) | Float |
| Conservation | GerpRSpval | Gerp element p-Value (default: 0) | Float |
| Conservation | bStatistic | Background selection score (default: 800) | Int |
| Conservation | ZooPriPhyloP | Primate PhyloP (43 genomes) scores | Float |
| Conservation | ZooVerPhyloP | Zoonomia PhyloP (241 genome) scores | Float |
| Conservation | ZooRoCC | Runs of Contiguous Constraint (RoCC) | Float |
| Conservation | ZooUCE | UltraConserved Elements (UCE) | Float |
| Epigenetics | EncodeDNase_max | Maximum Encode DNase-seq level (from 12 cell lines) (default: 0.0) | Float |
| Epigenetics | EncodeDNase_sum | Sum of Encode DNase-seq levels (from 12 cell lines) (default: 0.0) | Float |
| Epigenetics | EncodeH2AFZ_max | Maximum Encode H2AFZ level (from 13 cell lines) (default: 0.42) | Float |
| Epigenetics | EncodeH2AFZ_sum | Sum of Encode H2AFZ levels (from 13 cell lines) (default: 0.9) | Float |
| Epigenetics | EncodeH3K27ac_max | Maximum Encode H3K27ac level (from 14 cell lines) (default: 0.36) | Float |
| Epigenetics | EncodeH3K27ac_sum | Sum of Encode H3K27ac levels (from 14 cell lines) (default: 0.74) | Float |
| Epigenetics | EncodeH3K27me3_max | Maximum Encode H3K27me3 level (from 14 cell lines) (default: 0.47) | Float |
| Epigenetics | EncodeH3K27me3_sum | Sum of Encode H3K27me3 levels (from 14 cell lines) (default: 0.93) | Float |
| Epigenetics | EncodeH3K36me3_max | Maximum Encode H3K36me3 level (from 10 cell lines) (default: 0.39) | Float |
| Epigenetics | EncodeH3K36me3_sum | Sum of Encode H3K36me3 levels (from 10 cell lines) (default: 0.71) | Float |
| Epigenetics | EncodeH3K4me1_max | Maximum Encode H3K4me1 level (from 13 cell lines) (default: 0.37)Sum of Encode H3K4me2 levels (from 14 cell lines) (default: 0.73) | Float |
| Epigenetics | EncodeH3K4me1_sum | Sum of Encode H3K4me1 levels (from 13 cell lines) (default: 0.76) | Float |
| Epigenetics | EncodeH3K4me2_max | Maximum Encode H3K4me2 level (from 14 cell lines) (default: 0.37) | Float |
| Epigenetics | EncodeH3K4me2_sum | Sum of Encode H3K4me2 levels (from 14 cell lines) (default: 0.73) | Float |
| Epigenetics | EncodeH3K4me3_max | Maximum Encode H3K4me3 level (from 14 cell lines) (default: 0.38) | Float |
| Epigenetics | EncodeH3K4me3_sum | Sum of Encode H3K4me3 levels (from 14 cell lines) (default: 0.81) | Float |
| Epigenetics | EncodeH3K79me2_max | Maximum Encode H3K79me2 level (from 13 cell lines) (default: 0.34) | Float |
| Epigenetics | EncodeH3K79me2_sum | Sum of Encode H3K79me2 levels (from 13 cell lines) (default: 0.64) | Float |
| Epigenetics | EncodeH3K9ac_max | Maximum Encode H3K9ac level (from 13 cell lines) (default: 0.41) | Float |
| Epigenetics | EncodeH3K9ac_sum | Sum of Encode H3K9ac levels (from 13 cell lines) (default: 0.82) | Float |
| Epigenetics | EncodeH3K9me3_max | Maximum Encode H3K9me3 level (from 14 cell lines) (default: 0.38) | Float |
| Epigenetics | EncodeH3K9me3_sum | Sum of Encode H3K9me3 levels (from 14 cell lines) (default: 0.81) | Float |
| Epigenetics | EncodeH4K20me1_max | Maximum Encode H4K20me1 level (from 11 cell lines) (default: 0.47) | Float |
| Epigenetics | EncodeH4K20me1_sum | Sum of Encode H4K20me1 levels (from 11 cell lines) (default: 0.88) | Float |
| Epigenetics | EncodetotalRNA_max | Maximum Encode totalRNA-seq level (from 10 cell lines, minus and plus strand separately) (default: 0.0) | Float |
| Epigenetics | EncodetotalRNA_sum | Sum of Encode totalRNA-seq levels (from 10 cell lines always minus and plus strand) (default: 0.0) | Float |
| Epigenetics | GC | Percent GC in a window of +/- 75bp (default: 0.42) | Float |
| Epigenetics | CpG | Percent CpG in a window of +/- 75bp (default: 0.02) | Float |
| Mutability | freq100bp | Number of frequent (MAF > 0.05) gnomAD SNV in 100 bp window nearby (default: 0) | Int |
| Mutability | rare100bp | Number of rare (MAF < 0.05) gnomAD SNV in 100 bp window nearby (default: 0) | Int |
| Mutability | sngl100bp | Number of single occurrence gnomAD SNV in 100 bp window nearby (default: 0) | Int |
| Mutability | freq1000bp | Number of frequent (MAF > 0.05) gnomAD SNV in 1000 bp window nearby (default: 0) | Int |
| Mutability | rare1000bp | Number of rare (MAF < 0.05) gnomAD SNV in 1000 bp window nearby (default: 0) | Int |
| Mutability | sngl1000bp | Number of single occurrence gnomAD SNV in 1000 bp window nearby (default: 0) | Int |
| Mutability | freq10000bp | Number of frequent (MAF > 0.05) gnomAD SNV in 10000 bp window nearby (default: 0) | Int |
| Mutability | rare10000bp | Number of rare (MAF < 0.05) gnomAD SNV in 10000 bp window nearby (default: 0) | Int |
| Mutability | sngl10000bp | Number of single occurrence gnomAD SNV in 10000 bp window nearby (default: 0) | Int |
| Mutability | Roulette_MR | Mutability score from Roulette. MR: Roulette mutation rate estimate. | Float |
| Mutability | Roulette_AR | Mutability score from Roulette. AR: Adjusted Roulette mutation rate estimate. | Float |
| ProteinFunction | SIFTval | SIFT score (default: 0*) | Float |
| ProteinFunction | PolyPhenVal | PolyPhen2 score (default: 0*) | Float |
| ProteinFunction | dbscSNV_ada_score | Adaboost classifier score from dbscSNV (default: 0*) | Float |
| ProteinFunction | dbscSNV_rf_score | Random forest classifier score from dbscSNV (default: 0*) | Float |
| ProteinFunction | Grantham | Grantham score: oAA,nAA (default: 0*) | Float |
| ProteinFunction | mirSVR_Aln | mirSVR-Aln (default: 0) | Int |
| ProteinFunction | mirSVR_E | mirSVR-E (default: 0) | Float |
| ProteinFunction | mirSVR_Score | mirSVR-Score (default: 0*) | Float |
| ProteinFunction | MMSp_acceptor | *MMSplice score on acceptor module. | Float |
| ProteinFunction | MMSp_acceptorIntron | *MMSplice score on acceptorIntron module. | Float |
| ProteinFunction | MMSp_donor | *MMSplice score on donor module. | Float |
| ProteinFunction | MMSp_donorIntron | *MMSplice score on donorIntron module. | Float |
| ProteinFunction | MMSp_exon | *MMSplice score on exon module. | Float |
| ProteinFunction | SpliceAI_acc_gain | *The probability of the variant being splice-altering (acceptor gain) from SpliceAI. | Float |
| ProteinFunction | SpliceAI_acc_loss | *The probability of the variant being splice-altering (acceptor loss) from SpliceAI. | Float |
| ProteinFunction | SpliceAI_don_gain | *The probability of the variant being splice-altering (donor gain) from SpliceAI. | Float |
| ProteinFunction | SpliceAI_don_loss | *The probability of the variant being splice-altering (donor loss) from SpliceAI. | Float |
| ProteinFunction | CADD_rawScore | Raw score from CADD model | Float |
| ProteinFunction | CADD_phred | CADD PHRED Score | Float |
| ProteinFunction | EsmScoreMissense | Meta AI Evolutionary Scale Model (ESM-1v) for variant effects in missense. | Float |
| ProteinFunction | EsmScoreInFrame | Meta AI Evolutionary Scale Model (ESM-1v) for variant effects in InDels Inframe. | Float |
| ProteinFunction | EsmScoreFrameshift | Meta AI Evolutionary Scale Model (ESM-1v) for variant effects in InDels Frameshift. | Float |
| ProximityTable | minDistTSS | Distance to closest Transcribed Sequence Start (TSS) (default: 5.5) | int |
| ProximityTable | minDistTSE | Distance to closest Transcribed Sequence End (TSE) (default: 5.5) | int |
| ProximityTable | Dist2Mutation | Distance between the closest BRAVO SNV up and downstream (position itself excluded) (default: 0*) | Float |
| ProximityTable | Dst2Splice | Distance to splice site in 20bp; positive: exonic, negative: intronic (default:0) | int |
| RegSeq | RegSeq0 | CNN trained on open chromatin sequences of multiple tissues.RegSeq0 - HEK293T | Float |
| RegSeq | RegSeq1 | RegSeq1 - K562 | Float |
| RegSeq | RegSeq2 | RegSeq2 - HepG2 | Float |
| RegSeq | RegSeq3 | RegSeq3 - HeLa-S3 | Float |
| RegSeq | RegSeq4 | RegSeq4 - MC-7 | Float |
| RegSeq | RegSeq5 | RegSeq5 - iPS DF 19.11 | Float |
| RegSeq | RegSeq6 | RegSeg6 - GM23338 | Float |
| RegSeq | RegSeq7 | RegSeg7 - GC-matched background | Float |
| RegSeq | Aparent2 | APARENT2 score to describe human polyadenylation of 5’ and 3’UTR | Float |
| TranscriptionFactors | RemapOverlapTF | Remap number of different transcription factors binding (default: -0.5) | Int |
| TranscriptionFactors | RemapOverlapCL | Remap number of different transcription factor - cell line combinations binding (default: -0.5) | Int |
| TranscriptionFactors | motifECount | Total number of overlapping motifs (default: 0) | Int |
| TranscriptionFactors | motifDist | Reference minus alternate allele difference in nucleotide frequency within an predicted overlapping motif (default: 0) | Float |
| TranscriptionFactors | tOverlapMotifs | Number of overlapping predicted TF motifs | Float |