at DiagnosticPrimers.org we created a tool for performing batch checks for the presence of SNPs in predicted PCR primer binding sites. A single primer set can be checked when you are not registered. To use the tool, go to Analyse Primersets and then click the ‘Submit’ button. To check up to 500 primer sets at once, or to save your primers and results, log on to your subscriber account. If you do not have an account yet? Register here. More information about subscribing to DiagnosticPrimers.org can be found here.
Previously, SNPCheck provided such functionality, but since it stopped supporting the website and the tool we decided to implement a new tool. Our tool makes use of dbSNP as well as Genome Aggregation Database (gnomAD). Please see Analyse Primersets for the current used versions of these databases. Currently we only perform primer set checks on the human reference genome: hg19/GRCh37.