...
- Variant: the variant coded as chr:position ref/alt
- SNP Id: if the variant is included in dbSNP, this field will show the rsID, otherwise, it will be empty
- Genes: if the variant overlaps with a gene, the gene symbol will be displayed here, otherwise, it will be empty. If it overlaps with more than one gene, they will be listed separated by comma
- Type: type of variant, SNV (Single Nucleotide Variant), MNV (Multi-nucleotide Variant), CNV (Copy Number Variant), SV (Structural Variant) or INDEL (Insertion or deletion)
- Consequence Type: this is the predicted effect of the variant in the genome. If a variant has more than one consequence type (because it overlaps different transcripts and/or genes), the "worst" consequence will be displayed. Consequence types are also colour coded according to their impact to improve readability:
- High impact in red
- Moderate impact in orange
- Low impact in blue
- Modifier in green
Deleteriousness: It consists of three sub-columns - SIFT, Polyphen and CADD.
SIFT scores are classified into tolerated and deleterious. SIFT score takes values in the range [0, infinite[, the lower the values, the more damaging the prediction. Color code for SIFT predictions: Tolerated in green and Deleterious in red.
Polyphen scores are classified into benign, possibly damaging, probably damaging and possibly & probably damaging. To visualize the actual score value, Please leave the cursor over each tag . Polyphen score takes values in the range [0, 1[, the closer to 2, the more damaging the prediction. Color codes for polyphen predictions:
Probably damaging in red
Possibly damaging in orange
Benign in green
Unknown in black
The CADD column displays the the scaled CADD score. A scaled C-score of greater of equal 10 indicates that the substitution is predicted to be within the 10% most deleterious substitutions that you can do to the human genome, a score of greater or equal 20 indicates the 1% most deleterious and so on. If you would like to apply a cut-off on deleteriousness, it is suggested by the CADD authors to put a cutoff somewhere between 10 and 20. Maybe at 15, as this also happens to be the median value for all possible canonical splice site changes and non-synonymous variants. Scores equal or greater than 15 are displayed in red.
Conservation: It consists of three columns - PhyloP, PhastCons and GERP.
Positive PhyloP scores measure conservation which is slower evolution than expected, at sites that are predicted to be conserved. Negative PhyloP scores measure acceleration, which is faster evolution than expected, at sites that are predicted to be fast-evolving. Absolute values of phyloP scores represent -log p-values under a null hypothesis of neutral evolution.
PhastCons estimates the probability that each nucleotide belongs to a conserved element. The phastCons scores represent probabilities of negative selection and range between 0 and 1.
Positive GERP scores represent a substitution deficit (i.e., fewer substitutions than the average neutral site) and thus indicate that a site may be under evolutionary constraint. Negative scores indicate that a site is probably evolving neutrally. Some authors suggest that a score threshold of 2 provides high sensitivity while still strongly enriching for truly constrained sites.
- Population Frequency: Minor Allele Frequency (MAF) are shown for the given populations and studies in the config.js. According to the frequency range, they are classified as follows:
- Very Rare if MAF is less than 0.001 and it is displayed in bright red.
- Rare if MAF ranges from 0.001 to 0.005 and it is displayed in pale red.
- Average if MAF ranges from 0.005 to 0.05 and it is shown in light blue.
- Common if the MAF is greater than 0.05 and it is shown in dark blue.
- Phenotype: It displays the traits observed for the variants. The sources taken are ClinVar and Cosmic.
Variant detail
bla blaBy default, the first variant in the grid is selected and the tabs are loaded with information for that variant.
The tabs are
- Advanced Annotation:
- Genotype Stats:
- Genome Context:
- Beacon Network: