RVS queries



Paste a list of max. 10 variants using coordinates and ref/alt alleles. Alternatively, enter a chromosomal region to retrieve all variants found in that region.
Example for a single nucleotide variant: chr7:140453136A>T
Example for a chromosomal region: 7:140430000-140440000 — we accept regions of up to 10,000bp.


Limit: exonic non-synonymous all
Display only variants observed in 1000KG Ph3, ExAC, ESP6500, UK10K ALSPAC/TWINS, and/or Scripps Wellderly
Output: Display results for the canonical isoform only (where applicable)
Format: HTML JSON Excel

Enter up to 10 dbSNP IDs (rs numbers).

Output: Display results for the canonical isoform only; this will skip intergenic variants.
Format: HTML JSON

Enter up to 10 genes using HGNC symbols, and optionally describe the variant(s) you want to search for.
We accept HGVS nomenclature for specific CDS and protein changes, such as "c.1234A>C" or "p.Val600Glu" (three-letter code for amino acids, '*' for stop codon). Use a question mark ('?') as a wild card: to find all variants of BRAF valine 600, gene="BRAF" and variant="p.Val600?", which will return amino acid changes as well as matching indels, stop gained variants, etc.
You can also describe variants using the following keywords: deletion, insertion, stop gained, stop lost, frameshift, inframe, as well as "exon (number)". All keywords have to be separated by a comma from each other. Example: gene="TP53", variant="exon 5, frameshift, deletion". Keywords will overwrite settings for exonic, non-synonymous, where applicable.

Gene:
Variant:
 
Limit: exonic non-synonymous all
Display only variants observed in 1000KG Ph3, ExAC, ESP6500, UK10K ALSPAC/TWINS, and/or Scripps Wellderly
Display results for the canonical isoform only (where applicable)
Output: HTML JSON tab-delimited

Enter a phenotype or the name of a disease. We will search our database for known associations between any genetic variant and that phenotype/disease.
You can limit your search to a particular gene, using a HGNC symbol.

Disease:
Gene:
 
Limit: exonic non-synonymous all
Display only variants observed in 1000KG Ph3, ExAC, ESP6500, UK10K ALSPAC/TWINS, and/or Scripps Wellderly
Display results for the canonical isoform only (where applicable)
Output: HTML JSON tab-delimited

Queries by cohort will enable you to quickly run a differential mutation analysis by comparing cohorts. You can put together a "case" and a "control" group based on several studies, including populations where available. Select up to ten genes and we will search RVS for all variants in those genes (up to 5kbp up/downstream) that differ between the two groups.

While the basic functionality including populations indicated below is working, we are still developing this exploratory tool further; particularly, to include more (public) disease data.

Enter up to 10 genes using HGNC symbols:


Group 1 — "Control" Group 2 — "Case"
Populations considered healthy:
1000 Genomes total (WGS)
        1000 Genomes African
        1000 Genomes American
        1000 Genomes Asian
        1000 Genomes European
        1000 Genomes South Asian
ESP6500 total (WES)
        ESP6500 African American
        ESP6500 European American
Scripps Wellderly (WGS)
UK10K ALSPAC/TWINS (WGS)

Populations with phenotypes:
High risk BRCA population (MSSM) (WES)
TCGA BRCA (somatic)
TCGA BRCA (germline) (WES)

1000 Genomes total
        1000 Genomes African
        1000 Genomes American
        1000 Genomes Asian
        1000 Genomes European
        1000 Genomes South Asian
ESP6500 total
        ESP6500 African American
        ESP6500 European American
Scripps Wellderly
UK10K ALSPAC/TWINS


High risk BRCA population (MSSM)
TCGA BRCA (somatic)
TCGA BRCA (germline)

Odds ratio cutoff:
Limit: exonic non-synonymous all
Note that frequencies for populations marked (WES) are derived from whole exome sequencing. Comparisons should therefore be limited to 'exonic'.
Display results for the canonical isoform only (where applicable)
Use gamma version