VarCon

VarCon retrieves nucleotide sequences surrounding single nucleotide variants (SNVs) and computes splice site scores and HEXplorer profiles to assess potential effects on splicing regulation.

Key Features:

• Ensembl reference retrieval: Retrieves sequence neighborhoods from the Ensembl human reference genome for specified SNVs.
• Transcript table integration: Combines corresponding transcript table information to provide neighborhood sequences in coding and noncoding contexts.
• HGVS input support: Accepts SNV references using the Sequence Variant Nomenclature (http://varnomen.hgvs.org/) for unambiguous identification.
• Splice site scores: Computes and displays splice site scores including HBond and MaxEnt metrics.
• HEXplorer profiles: Generates HEXplorer profiles that show position-dependent splice enhancing and silencing properties within the SNV neighborhood.

Scientific Applications:

• Splicing impact assessment: Evaluates how SNVs may alter splice site recognition and splicing regulation using sequence context and score metrics.
• Pathogenic variant identification: Aids identification of variants that potentially cause disease through disrupted splicing patterns.
• Therapeutic target exploration: Supports investigation of nucleotide changes that could modulate splice site activity for therapeutic strategies.

Methodology:

Accepts an SNV reference (Sequence Variant Nomenclature), retrieves the sequence neighborhood from the Ensembl human reference genome and transcript table, and processes these data to generate HBond and MaxEnt splice site scores and HEXplorer profiles.