Add varSEAK splicing links to VCI

[cgpreston]

Add a varSEAK tool link in the splicing sections in the Variant Type tab.

DRAFT specifications:

1. If possible construct the URL based on the variant's: Gene (HGNC Gene Symbol, e.g. CFTR) RefSeq transcript (most likely the transcript used to construct the variant title, e.g. NM_000492.4) HGVS c.nomenclature (also found in variant title, e.g. c.1585-8G>A)
   • example URL: https://varseak.bio/ssp.php?gene=CFTR&transcript=NM_000492.4&variant=&hgvs=c.1585-8G>A
   • varSEAK is mapped to hg19, however it is transcript based. RefSeq transcripts and Ensembl transcripts are both supported.
2. If number 1 option is not possible (e.g if there is no gene or the transcript is not discernible.... i.e. no gene symbol or no c. nomenclature in variant title), direct users to the primary site (https://varseak.bio/).

Consider adding link to varSEAK documentation/blurb about varSEAK (Jenny to draft?)

2047

https://broadinstitute.atlassian.net/browse/CSP-54

[jennygoldstein]

Here are a couple of blurbs (one very short and one longer) about varSEAK, including the link to the documentation and video. I think either blurb is fine to use, depending on the context. Does this look OK?

Short version: "VarSEAK provides the JSI splice site prediction tool to predict the splicing effects of genetic variants. For more information on this tool and how to use it, see https://varseak.bio/pdf/SSP-Documentation.pdf and https://www.jsi-medisys.de/products/varseak/varseak-online/”

Longer version: "VarSEAK provides the JSI splice site prediction tool to predict the splicing effects of genetic variants impacting canonical splice sites (i.e. with core motif GT for 5' donor splice sites or AG for 3' acceptor splice sites). This tool gives a splice predictor class, a table with relevant splice site positions with a splice site score and MaxEntScan ENT score, as well as differences in scores for the reference sequence compared to the variant. The interface provides a sequence graphic to facilitate interpretation of the results. For more information on this tool and how to use it, see https://varseak.bio/pdf/SSP-Documentation.pdf and https://www.jsi-medisys.de/products/varseak/varseak-online/”

[wrightmw]

Replaced by https://github.com/ClinGen/gene-and-variant-curation-tools/issues/58