InterVar specifications


Unique identifier OMICS_24124
Name InterVar
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data A list of variants that are already annotated with a set of required information.
Input format TSV
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Version 1.0.8
Stability Stable
Maintained Yes



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  • person_outline Kai Wang <>

Publication for InterVar

InterVar in publications

PMCID: 5938035
PMID: 29700284
DOI: 10.1038/s12276-018-0079-0

[…] for the interpretation of sequence variants by the american college of medical genetics and genomics and the association for molecular pathology,, we manually analyzed this variant using an intervar model, and the results also suggested that this variant was pathogenic., on the basis of these results, we generated an ipo13-deficient animal model to dissect the roles of ipo13 in ocular […]

PMCID: 5919682
PMID: 29659569
DOI: 10.1371/journal.pgen.1007355

[…] (). following the guidelines from the american college of medical genetics and genomics and the association for molecular pathology (acmg-amp) for variant interpretation and classification [] using intervar [], all the missense variants here identified in atm, chek2, brip1 and tp53 are classified as vus. adding the ps3 criterion (“well-established in vitro or in vivo functional studies […]

PMCID: 5933375
PMID: 29683450
DOI: 10.3791/57266

[…] likely benign; or 5) benign. note: for the purposes of ondri, an in-house designed python script is used to perform acmg classification on a semi-automated basis. although not used for this study, intervar is a similarly designed tool that can be utilized in an analogous manner., sanger sequence any variants with a sequencing coverage of <30x and/or variants that have been identified […]

PMCID: 5869741
PMID: 29619247
DOI: 10.1038/s41525-018-0048-5

[…] through haplotype caller for each patient were further subject to interpretation based on acmg/amp standards and guidelines for the interpretation of sequence variants. this was preformed through intervar(version 0.1.7), a software program designed to assess the pathogenicity of the variants according to acmg/amp standards and guidelines. the pathogenicity of identified variants […]

PMCID: 5902396
PMID: 29368431
DOI: 10.1002/mgg3.357

[…] et al., ). the patient was diagnosed with ebstein anomaly; her father, who has mild ebstein anomaly, was found to carry the variant as well. this variant was not found in exac. using the acmg intervar classification tool, this variant was considered of uncertain significance (li & wang, ). in patient 34, a variant was found in exon 2 of gata6, c.c15g (p.asp5glu), which was inherited […]

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InterVar institution(s)
Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA, USA; Institute for Genomic Medicine, Columbia University, New York, NY, USA; Department of Biomedical Informatics, Columbia University, New York, NY, USA
InterVar funding source(s)
Supported by NIH grants HG006465 and MH108728.

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