PopViz

PopViz

Integrative and interactive visualization of population genetics and mutation deleteriousness of human genes
 
( gnomAD exomes.r2.1.1 and genomes.v3.1.2, with CADD v1.6 )
 
Reference: Zhang P., et al. PopViz: a webserver for visualizing minor allele frequencies and damage prediction scores of human genetic variations. Bioinformatics. 2018.
 
[PMID:30535305] [Paper]


gnomAD version:
r2.1.1(125,748 exomes)
v3.1.2(76,156 genomes)

Human reference genome:
GRCh37
GRCh38

MAF (minor allele frequency):
General
Maximum
AFR:African / African American
AMR:Admixed American / Latino
ASJ:Ashkenazi Jewish
EAS:East Asian
FIN:Finnish
NFE:Non-Finnish European
SAS:South Asian

Variant consequence:
MisLOF (missense, frameshift, stop-gain, start/stop-loss, essential splicing, IVS-pLOF)
All MisLOF + (inframe-indel, splice region, intronic, synonymous, UTR)

MSC (mutation significance cutoff) on CADD v1.6: None CI:99% CI:95% CI:90%

Only variants that are in more than 1 individual (not singleton, AC > 1)

Only variants that exist homozygous alleles (HOM >= 1)

User's varaints? No Yes

Please provide the first 5 columns (CHROM, POS, ID, REF, ALT) of the varaints in VCF format. If no ID, fill it with a dot. It's required to provide the computed CADD scores for your variants, into the 6th column. Please be consistent with the reference genome and CADD versions.


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Developer| Peng ZHANG   Ph.D.

Lab Head| Jean-Laurent CASANOVA   M.D., Ph.D.

Laboratory| St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University

Last Update| March 15, 2023

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The Rockefeller University, New York, USA