• ClinGen Variant Curation Interface (VCI) - Used to perform curations. Can use demo version without an account. Broad has specific affiliation (contact msingerb@broadinstitute.org for more information)

• ClinGen Allele Registry - Generates unique variant ID for VCI input (alternatively can use Clinvar ID if available). Allele registry variant ID's are also found on the gnomAD variant page for variants in gnomAD

• Interpreting Genomes for Rare Disease Course 2018 Recordings - Videos available on curation (gene and variant) and overall genome interpretation

• Seqr - Where RGP and CMG/Gregor WES/WGS data are analyzed for causative variants

• gnomAD - Database of variation in controls from case-control studies with exome and genome data, used to check MAF, expression and transcripts

• NCBI: ClinVar - Database of variant classification submissions

• NCBI: PubMed - Search engine for scientific literature

• OMIM - database of genes and diseases and relevant information for both

• UCSC Genome Browser - Browser to visually inspect regions of the genome

• LoF Curation portal - used to perform LoF curations

• Decipher - Database of variation and another tool for gene/genome visualization

• HGMD - Database of variation with relevant literature for each variant

• GenCC database - Database of gene curations across organizations

• SpliceAI tool - Tool to provide spliceAI scores for any variant

• Alamut - Tool to check splicing predictions (see #alamut slack channel for download instructions)

• SV/CNV calculator - tool to perform SV/SNV curations

To perform a thorough literature search you need to search using all possible nomenclature for a variant and gene. It is often beneficial to first check ClinVar and HGMD for papers that have already been identified with the variant in question. Newer reports will not be included in these submissions and other data could have been missed by prior curation so it is important to ALWAYS perform your own literature search. This includes the "c." and "p." nomenclature for all missense variants, as well as the single letter (e.g. p.R123P) and 3 letter amino acid code (p.Arg123Pro) when searching the "p." nomenclature. It can be often useful to use the "c." and "p." nomenclature without search using the letter code to be more inclusive of search results (e.g. 123G>A instead of c.123G>A or Arg123Pro instead of p.Arg123Pro). For intronic (including splice site) variants there is no "p." nomenclature so only one search term is required. Frameshift variants have a more complicated nomenclature, but the "c." is probably the best way to find literature. However, combinations of the "p." nomenclature should also be searched (e.g. p.Arg123fs, p.Arg123ProfsX etc.). For nonsense variants there is also additional nomenclature so searching using all possible names, using 1 and 3 letter codes is important (e.g. p.Arg123X, p.Arg123*, p.Arg123Ter). The best search engine is usually google scholar over pubmed. If there are multiple gene names it is also important to search using any that might still be in use. For example, SELENON is still referred to as SEPN1 in the literature. Older gene names that are no longer in use do not usually need to be searched.

https://github.com/ClinGen/clincoded/wiki/VCI-Curation-Help - If you want a live demo of the VCI you can contact any curation team member for assistance (see Home page for contact details)

https://cmg.broadinstitute.org/using-seqr