HGMD, ANNOVAR and Genome Trax releases – Fall


QIAGEN Digital Insights

HGMD, ANNOVAR and Genome Trax releases – Fall

HGMD Professional

The fall release of HGMD Professional now contains a total of 214,158 mutation entries. That’s 5,790 more mutation entries than the previous release. Unlike other mutation databases, HGMD mutations are all backed by peer-reviewed publications where there is evidence of clinical impact.

View the complete HGMD statistics

New HGMD feature

The original extended cDNA sequences were only available for a small number of genes, and have been out of date for some time. We have now added a link to a new extended cDNA sequence for each gene based on hg38 sequence and annotations. The sequence is shown split between the full exonic sequence in uppercase, and 50 bp of flanking intronic sequence in lowercase. Exon numbering is sequential. This feature is under ongoing development, and we plan to add in further CDS annotations at a later date. The old extended cDNA sequences, along with the old mutation viewer will be removed from HGMD Professional for the 2018.1 release.

If you are interested into a clinical-grade pathogenicity assessment for a given variant implementing the ACMG guidelines and including additional supporting data such as case counts in a hereditary cancer context, we recommend you take a look at QIAGEN Clinical Insight for Hereditary Cancer, which includes HGMD.  The following is a table summarizing key features between HGMD Public, Pro, and QIAGEN Clinical Insights (QCI).


2017 July 16
ANNOVAR new version is available now! You can use the old link to download, or you can register again to get download email. This release contains some minor fixes and improvements: fixed a bug in calculating upstream distance that print when -separate is specified in annotate_variation.pl, improvements to coding_change.pl to report more stopgain/stoploss and fix use-of-uninitialized-value issue, slight change to convert2annovar.pl to handle mal-formed VCF file.

2017 September 12
There is now an hg38 version of ensGene available through ANNOVAR directly so that users do not need to build it themselves.

2017 September 29
2017Sep29: avsnp150 is available through ANNOVAR now in hg19 and hg38 coordinate, to annotate your variants with dbSNP identifiers.

2017 October 13
Latest clinvar (20170905) is available now through ANNOVAR in hg19 and hg38 coordinates. A long-standing problem on multi-allelic variants in ClinVar is now addressed, so that multi-allelic variants are now correctly assigned to the corresponding benign/pathogenic categories. The 20170130/20170501 versions are also updated to resolve this issue.

Learn more about how ANNOVAR can be used with HGMD for variant annotation.

Genome Trax

Updated tracks have been released concurrent with the HGMD release for all HGMD-related tracks. Additional major tracks updated include TRANSFAC® release 2017.3, and PROTEOME™ release 2017.3. Release notes can be found here.