Tag Archives: Variant Classification

VarSeq Update: Support for the Interpretation of Non-coding and Splice Site Variants

         April 15, 2021
Splice site

While VarSeq has always had excellent support for variant interpretation and analysis, we continue to find new edge cases in the clinical literature that improve our interpretation capabilities. In this blog, we will be covering some of the new improvements in VarSeq to support the interpretation of non-coding and splice site variants. Transcript Annotation Improvements Let’s start by covering some… Read more »

Webcast Recap: VSWarehouse: Tracking Changing Variant Evidence and Classifications

         March 11, 2021
VSWarehouse

Thank you to those who attended the recent webcast, “VSWarehouse: Tracking Changing Variant Evidence and Classifications”. For those who could not attend but wish to watch, here is a link to the recording. The webcast covered some general highlights of VSWarehouse value but also presented some specific capabilities covering the ClinVar classification tracker. Golden Helix provides complete solutions to handle… Read more »

Clinical Variant Analysis: Part V

         March 5, 2019

Examples of Clinical Variant Interpretation with VSClinical In this chapter, I’d like to go through a few examples for variants that have been classified with the help of VSClinical. This will give you a better understanding of how data sources are actually being represented in the software and how those are used to make decisions on applicable criteria. It goes… Read more »

Clinical Variant Analysis: Part IV

         February 28, 2019

Rules for Combining Various Classification Criteria Now that we have a solid understanding of how the various criteria are meant to be applied, it’s time to look at how the evidence collectively leads to the clinical categorization of a variant. Let’s go through the rule framework for combining the various criteria. Pathogenic In order for a variant to be classified… Read more »

Clinical Variant Analysis: Part III

         February 26, 2019

Clinical Variant Analysis – Classification Criteria of Benign Variants The classification of benign variants is overall simpler and more straightforward, with the majority of benign variants being eliminated through allele frequency in various population catalogs. BA1 If a variant is common in one or more population catalog, as indicated by the allele frequency associated by the appropriate sub-population, it can… Read more »

Clinical Variant Analysis: Part II

         February 25, 2019

Clinical Variant Analysis – Classification Criteria of Pathogenic Variants The ACMG Guidelines are utilized for the interpretation of variants. They are primarily applied to diagnose suspected inherited (primarily Mendelian) disorders in a clinical diagnostic laboratory setting. While evaluating variants no matter what the origin, it is important to distinguish between variants that are pathogenic (i.e., causative) for a disease and a… Read more »

The State of Variant Annotation: A Comparison of AnnoVar, snpEff and VEP

         June 25, 2014

Up until a few weeks ago, I thought variant classification was basically a solved problem. I mean, how hard can it be? We look at variants all the time and say things like, “Well that one is probably not too detrimental since it’s a 3 base insertion, but this frameshift is worth looking into.” What we fail to recognize is… Read more »