Interpret Structure Variant

 InterSV - Structure Variant Interpretation

Evidence system

ACMG introduces a quantitative, evidence-based scoring framework; encourages the implementation of the five-tier classification system widely used in sequence variant classification; and recommends "uncoupling" the evidence based classification of a variant from its potential implications for a particular individual.The ACMG professional standards will guide the evaluation of constitutional CNVs and encourage consistency and transparency across clinical laboratories. We aligned and extended these ACMG/AMP/ClinGen guidelines for structure variants(SVs). The evidence category include: 1.Initial assessment of genomic content;2.Established (or Predicted) Pathogenic or Benign Dosage Sensitive Genes/Genomic Regions;3.Evaluation of Gene Number;4.Detailed Evaluation of Genomic Content Using Cases from Published Literature, Public Databases;5.Evaluation of Inheritance Pattern/Family History.

Score system

The standards build by introducing a semiquantitative point-based scoring metric for classification. In general,scores for each observed piece of evidence, both in support of (positive values) and refuting (negative values) pathogenicity, are summed to arrive at a final classification. SVs with a final point value >=0.99 are considered pathogenic, while point values between 0.90 and 0.98 are consided likely pathogenic; The variant of uncertain significance (VUS) category is the broadest, corresponding to points between −0.89 a 0.89 ,while refutinnng evidence arriving at scores between −0.9 and 0, <=-0.90 are considered likely benign and benign, respectively.


The URL for direct linking to specific variants with genomic version and proper variant information.

Before the variant searching, the user need to know the genomic version(currently, support hg19 and hg38) and variant type. InterSV support 3 types of structure variants: deletion(del), duplication(dup) and translocation(ctx).
if you want to put systematic URL links on your web server registry for each variant with one click,
here is the method:
Assumed your variant is located in chromosome 1, the coordinate of start is 2641431 (hg19), the coordinate of end is 29746184 , the variant type is del,then the systematic URL link will be:
"" click to test
This URL will bring you to the interpretation page directly, also with all automated criteria.
If you want to adjust the interpretation, you need to start from the server.

Please cite:

Quan Li, YunYun Zhou and Kai Wang. InterSV: a web server for evidence-based clinical interpretation of structure variants. (In Preparation,2021)
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