Welcome to the VICC classification platform
This webpage provides a collection of somatic variants. Each variant is annotated by a wide variety of databases and computational scores. Utilizing these allows users to classify a variant in one of five classes (benign-oncogenic). You can not register yourself. If you need access or want to contribute to VICC-CP please ask a member of the consortium.Overview
Currently, the VICC-CP has- 23697 total variants
- 23639 classified variants
- 337 variants with multiple classifications
- 68 variants with multiple different classes
- 269 variants with multiple identical classes
- These classifications are across 4 cancertypes
- And were classified by 9 users
Annotations
Title |
Description |
Version |
Version date |
|---|---|---|---|
| rs-num | The rs-number of a variant from dbSNP (version summary: https://www.ncbi.nlm.nih.gov/projects/SNP/snp_summary.cgi) | 155 | 2021-06-16 |
| PhyloP-100way | PhyloP 100 vertebrates (100-way) conservation scores. These scores measure evolutionary conservation at individual alignment sites. Interpretations of the scores are compared to the evolution that is expected under neutral drift. Positive scores: Measure conservation, which is slower evolution than expected, at sites that are predicted to be conserved. Negative scores: Measure acceleration, which is faster evolution than expected, at sites that are predicted to be fast-evolving. | - | 2013-12-01 |
| CADD | The scaled CADD scores: PHRED-like (-10*log10(rank/total)) scaled C-score ranking a variant relative to all possible substitutions of the human genome (8.6x10^9). These scores range from 1 to 99. A cutoff for deleteriousness can be set to 10-15, but the choice remains arbitrary. | v1.6 | 2020-04-11 |
| REVEL | The REVEL pathogenicity score of this variant. This score can range from 0 to 1, which reflects the number of trees in the random forest that classified the variant as pathogenic. Thus, higher values represent a more "certain" decision. When choosing a cutoff one should keep in mind that higher cutoffs will result in a higher specificity, but lower sensitivity. | v1.3 | 2021-05-03 |
| spliceAI | Details about the SpliceAI predictions: These include delta scores (DS) and delta positions (DP) for acceptor gain (AG), acceptor loss (AL), donor gain (DG), and donor loss (DL). Format: GENE|DS_AG|DS_AL|DS_DG|DS_DL|DP_AG|DP_AL|DP_DG|DP_DL | v1.3.1 | 2021-09-07 |
| spliceAI max delta | Max of delta scores for acceptor gain, acceptor loss, donor gain and donor loss. A value of 0.5 or more can be assumed to have an impact on splicing. | v1.3.1 | 2021-09-07 |
| allele count | gnomAD alternate allele count for samples | v3.1.2 | 2021-10-22 |
| allele frequency | gnomAD frequency of alternate allele in samples | v3.1.2 | 2021-10-22 |
| hom | gnomAD number of homozygous individuals in samples | v3.1.2 | 2021-10-22 |
| hemi | gnomAD number of hemizygous individuals in samples | v3.1.2 | 2021-10-22 |
| het | gnomAD number of heterozygous individuals in samples | v3.1.2 | 2021-10-22 |
| popmax | gnomAD population with maximum allele frequency (AF) | v3.1.2 | 2021-10-22 |
| mito AC hom | Allele count restricted to variants with a heteroplasmy level >= 0.95 from the GnomAD mitochondrial genome data. These variants are (almost) homozygous among all mitochondria in an individual | v3.1 | 2020-11-17 |
| BRCA exchange | Variant pathogenicity as displayed in the Summary view of the BRCA exchange database | 54 | 2022-02-22 |
| cancertypes | A | delimited list of all cancertypes associated to this variant according to cancerhotspots. FORMAT: tumortype:tissue | v2 | 2017-12-15 |
| allele count | Number of samples showing the variant from cancerhotspots | v2 | 2017-12-15 |
| allele frequency | Allele Frequency of the variant (AC / num samples cancerhotspots) | v2 | 2017-12-15 |
| class | Family classification: LFS = strict clinical definition of Li-Fraumeni syndrome, LFL = Li-Fraumeni like for the extended clinical definition of Li-Fraumeni, FH: family history of cancer which does not fulfil LFS or any of the LFL definitions, No FH: no family history of cancer, FH= Family history of cancer (not fulfilling the definition of LFS/LFL), No= no family history of cancer, ?= unknown | r20 | 2019-07-01 |
| DNE LOF class | Functional classification for loss of growth-suppression and dominant-negative activities based on Z-scores | r20 | 2019-07-01 |
| DNE class | Dominant-negative effect on transactivation by wild-type p53. Yes: dominant-negative activity on WAF1 and RGC promoters, Moderate: dominant-negative activity on some but not all promoters, No: no dominant-negative activity on both WAF1 and RGC promoters, or none of the promoters in the large studies. | r20 | 2019-07-01 |
| domain function | Function of the domain in which the mutated residue is located. | r20 | 2019-07-01 |
| transactivation class | Functional classification based on the overall transcriptional activity | r20 | 2019-07-01 |
| popmax AF | The allele frequency of the "popmax" population | v3.1.2 | 2021-10-22 |
| HCI prior | The prior probability of pathogenicity as reported in the priors HCI website. These range from 0.97 for variants with high probability to damage a donor or acceptor to 0.02 for exonic variants that do not impact a splice junction and are unlikely to create a de novo donor. | 1 | 2022-11-15 |
| cmc significance tier | The COSMIC significance tier. Can have values from 1-3 or orther, no tier | v7 | 2020-10-27 |
| classification | The final classification resulting from the codes provided by ClinGen | - | 2023-03-31 |
| codes | The applied criteria from ClinGen | - | 2023-03-31 |
| CHASMplus | The CHASMplus p-value. Lower p-value means that the variant is more likely to be oncogenic | v1.0.0 | 2020-06-19 |
| VEST4 | The VEST4 p-value | v4 | 2013-02-20 |
| fathmm-xf | The fathmm-xf score | 1.0.2 | 2018-02-01 |
| chasm transcript | The transcript which belongs to the CHASMplus score | v1.0.0 | 2020-06-19 |
| vest transcript | The transcript which belongs to the VEST4 score | v4 | 2013-02-20 |
| cosmic-id | The cosmic variant id | - | 2023-04-27 |
| civic-id | The CIVIC variant id | v3.0.0 | 2023-04-21 |
| civic | The CIVIC assertions and evidences from the simple molecular profile | - | 2023-07-03 |
| MaxEntScan | The transcript specific MaxEntScan scores calculated from ngs-bits. | v1.0.0 | 2023-09-27 |
| MaxEntScan SWA | The transcript specific MaxEntScan SWA scores calculated from ngs-bits. A special application of the MaxEntScan algorithm to discover de-novo spliceing variants. | v1.0.0 | 2023-09-27 |
| ClinVar variation ID | The Variation ID from ClinVar | - | 2023-02-26 |
| AlphaMissense | The Alpha Missense pathogenicity score. <0.34 = likely benign, >0.56 = likely pathogenic, <=0.34 & >=0.56 = ambigous. | v1.0.0 | 2023-09-22 |
| popmax AC | The allele count from the popmax population from GnomAD | v3.1.2 | 2021-10-22 |
| BayesDEL | Missense variant functional predictions by BayesDel tool (Feng 2017) used without allele frequency. Score bigger or equal to 0.16: damaging; Score smaller than 0.16: tolerated. Scores were imported from dbNSFP. | 4.4 | 2023-05-06 |
| Pfam protein domains | The Pfam protein domain accession ids of all transcripts. Multiple values are separated with , - symbols. This data is generated by VEP. | 110 | 2023-07-18 |
| cancertype same position | A | delimited list of all cancertypes associated to this variant according to cancerhotspots. FORMAT: tumortype:tissue. These are all changes at the same amino acid position independent of the amino acid exchange. | v2 | 2017-12-15 |
| class | The oncogenicity from OncoKB | v4.27 | 2025-03-28 |
| effect | The mutation effect from OncoKB | v4.27 | 2025-03-28 |
| recurrence_same_aa | The number of mutated samples at the amino acid position of this variant which causes the same amino acid exchange | v7 | 2020-10-27 |
| recurrence_same_pos | The number of mutated samples at the amino acid position of this variant in COSMIC | v7 | 2020-10-27 |
Changelog
v 1.9
WARNING: VICC-CP is currently in "privacy mode" this means that you can only see your own classifications. VICC-CP will return to normal when the interlaboratory comparison test is over.
General changes:
- Improved cancerhotspots annotation - it is now based on the amino acid position
- Switched from VEP consequence calculation to ngs-bits VcfCalculateConsequence tool (GitHub)
- SBVS1 and SBS1 are now mutually exclusive
Bugfixes:
previous changelog
- Fixed an issue when two criteria had the same mutually exclusive criterion target and both were selected. If the use would unselect one of them the mutually exclusive criterion would be enabled for selection even though it shouldn't
- REVEL scores are now shown properly on the variant classify page
- Fixed a bug where sometimes wrong links to COSMIC would be generated
- Fixed a bug where in some cases the COSMIC CMC tier would not be shown
- Fixed a bug where OS1 would be automatically selected even though the pathogenic variant is not within an exon