Abstract Motivation Genome sequencing has had a remarkable impact on our ability to study the effects of human genetic variation, however, variant interpretation remains the major bottleneck. Understanding the potential impact of variants, including structural variants, requires extensive annotation from disparate sources of knowledge, and in silico prediction algorithms. Results We introduce Seave, an intuitive web platform that enables all types of variants to be securely stored, annotated and filtered. Variants are annotated with allele frequencies and pathogenicity assessments from many popular databases and in silico pathogenicity prediction scores. Seave enables filtering of variants with specific inheritance patterns, including somatic variants, by quality, allele frequencies and gene lists which can be curated and saved. Seave was made for whole genome data and is capable of storing and querying copy number and structural variants. Availability and implementation To demo Seave with public data, see https://www.seave.bio. Source code is available at http://code.seave.bio and extensive documentation is available at http://documentation.seave.bio. Seave can be locally installed on an Apache server with PHP and MySQL, or we provide an Amazon Machine Image for quick deployment. For commercial and clinical diagnostic licensing, contact the corresponding author. Supplementary information Supplementary data are available at Bioinformatics online.