This app is being upgraded and is not currently available. Instead, please use Data Viewer Plus, which is new functionality at Sequencing.com that provides similar information as this app.
Clinical annotations of genomic variants
This app analyzes human genetic data and provides clinical annotations of variants that is consistent with the principles of the Human Genome Variation Society (HGVS) guidelines.
The app utilizes multithreaded cloud computing technology to provide clinical annotations for almost all genetic data (Next-Generation Sequencing (NGS) including Whole Genome and Exome as well as genotyping microarrays).
This app is being upgraded and is not currently available. Instead, please use Data Viewer Plus, which is new functionality at Sequencing.com that provides similar information as this app.
Log in to your Sequencing.com account and click the 'Add to My Apps' button located under the app icon. This app will instantly be added to your account and a 'Start App' button will appear under the app icon.
Once the app finishes you'll receive an email with a link to the results. You can also access results at any time by clicking Apps in the header and then clicking the Results tab.
Inputs
Outputs
Multiallelic calls and/or multiple transcripts
Every line of the output CSV file represents a single variant call. Unlike in the VCF format, annotation information for multiallelic variant calls are split to multiple lines (Example 1). If a variant call overlaps with multiple transcripts, the information is also split into multiple records (Example 2).
Example 1
For the single VCF record describing a 1-base deletion and a 1-base insertion:
#CHROM | POS | ID | REF | ALT | Additional columns... |
8 | 3443799 | . | GA | G,GAA | Additional data... |
two lines will be added to the output CSV file:
ID | CHROM | POS | REF | ALT | QUAL | FILTER | TYPE | ENST | GENE | Additional columns... |
. | 8 | 3443799 | GA | G | 42 | PASS | Deletion | ENST00000537824 | CSMD1 | Additional data... |
. | 8 | 3443799 | GA | GAA | 42 | Pass | Insertion | ENST00000537824 | CSMD1 | Additional data... |
The TYPE and CSN annotation flags are given as follows:
Example 2
For the single VCF record describing a triallelic substitution that overlaps with two transcripts (ENST00000325203 and ENST00000344683) in the whole exome set:
#CHROM | POS | ID | REF | ALT | Additional columns... |
8 | 6389889 | . | C | G,A | Additional data... |
four lines will be added to the output CSV file:
ID | CHROM | POS | REF | ALT | QUAL | FILTER | TYPE | ENST | GENE | Additional columns... |
. | 8 | 6389889 | C | G | 200 | PASS | SUBSTITUTION | ENST00000325203 | ANGPT2 | Additional data... |
. | 8 | 6389889 | C | G | 200 | PASS | SUBSTITUTION | ENST00000344683 | MCPH1 | Additional data... |
. | 8 | 6389889 | C | A | 200 | PASS | SUBSTITUTION | ENST00000325203 | ANGPT2 | Additional data... |
. | 8 | 6389889 | C | A | 200 | PASS | SUBSTITUTION | ENST00000344683 | MCPH1 | Additional data... |
The GENE, LOC and CSN annotation flags are given as follows:
This app utilizes CAVA v1.1.0.
Márton Münz, Elise Ruark, Anthony Renwick, Emma Ramsay, Matthew Clarke, Shazia Mahamdallie, Victoria Cloke, Sheila Seal, Ann Strydom, Gerton Lunter, Nazneen Rahman. (2015) CSN and CAVA: variant annotation tools for rapid, robust next-generation sequencing analysis in the clinical setting. Genome Medicine 7:76, doi:10.1186/s13073-015-0195-6.