This page provides information that is likely to be useful to professionals in clinical genetics/genomics e.g. information about individual clinical conditions (GeneReviews, OMIM and Orphanet), individual genetic variants (DECIPHER, LOVD, ClinVar, HGMD, VarSome, CanVar & VEP), transcript identification (LRG) and variant nomenclature (HGVS).  Professionals are also likely to find sources that are listed on other pages here  to be of relevance and interest, particularly the Universities page (including the genome browsers) and the Ethical, Legal and Social Implications page.

GeneReviews

This database contains a large number of reasonably comprehensive, disease-orientated, reviews. They are generally expert-authored and easy to read, containing clinical features, differential diagnoses and molecular details.  

OMIM

An online, highly detailed, reference catalogue, listing human genetic conditions & their related genes. Initially compiled by the late Victor McKusick it now contains >24,000 entries & includes valuable links to other databases e.g. ClinVar. 

Orphanet

A portal for rare diseases & orphan drugs. 
Database of numerous short articles regarding rare diseases and disease genes.
​Organisation is based in Paris.

DECIPHER

An interactive database with a suite of tools to aid interpretation of genomic variants. It retrieves information from a variety of bioinformatics resources. To help interpretation, a patient’s variant is displayed together with levels of normal variation and pathogenic variation at that locus.

LOVD

Leiden Open Variation Database (LOVD): an online gene-centered collection and display of DNA variations. Contains a large body of variant data plus valuable updated details of, and links to, an enormous number of other international DNA variant databases.

ClinVar

A database of genetic variants, based at the NCBI in USA, containing in a single database, hundreds of thousands of records, regarding specific gene variants, the degree of pathogenicity of each variant and the evidence supporting that.

gnomAD (genome Aggregation Database)

The genome Aggregation Database (gnomAD) contains over 120,000 exome sequences plus over 15,000 whole-genome sequences. It is far larger than ExAC (containing approximately 60,000 exomes), which preceded gnomAD.

Human Genome
​Variation Society

The HGVS provides helpful guidelines for describing specific variants in DNA, RNA and proteins, according to internationally agreed standards.  A relatively brief "simple" summary can be found here. 

Locus Reference
​Genomic 

A database, supported by EMBL and NCBI, providing non-changing gene and transcript identifiers. Increasingly used by laboratories to determine which specific transcript is to be used when reporting gene variants. 

Human Gene
​Mutation Database

The HGMD at Cardiff in Wales, UK, is an attempt to collate all published gene lesions responsible for human inherited disease. The full (professional) database requires a subscription but academics can access the less up-to-date but still useful, version.

Glossary & Quiz Apps
for Clinical Genomics​

Free glossary app, containing brief illustrated explanations of >40 frequently-used terms e.g. "FASTQ, BAM, VCF, gVCF, Phred, BED, BWA & GATK".  Also an accompanying self-assessment quiz app. Both apps function offline & are used as reminders by students & professionals, internationally.  

European 
Reference Networks

Virtual networks involving Reference Centers across Europe. They aim to tackle complex or rare conditions by convening a “virtual” advisory board of medical specialists to review a patient’s diagnosis & treatment.

Genetic/genomic variant interpretation

VarSome DNA variant analysis

VarSome provides analysis of individual genetic variants, one at a time. Permitted input formats include HGVS nomenclature for DNA-level and protein (amino acid) level variants (but not protein-level frameshift variants entries, as not sufficiently specific). Also provides automated variant interpretation using ACMG-guidelines. 

Cancer predisposition gene Variant Database​

A resource for cancer predisposition gene variant interpretation. Uses multiple data sources to classify variants, including shared data from NHS diagnostic laboratories on BRCA variants to enable case:control comparisons with population data. Includes both automated and curated classifications. Contains links to functional analyses eg saturation genome editing BRCA1 haploid cell assay.

Variant Effect Predictor (VEP)

Variant Effect Predictor (VEP), part of the Ensembl Genome Browser, provides automated interpretation of single or multiple genetic variants. It provides Polyphen and SIFT analysis scores and also provides frequency data from ExAC and gnomAD.

Localized/national initiatives

England
Health Education England: Genomics Education Programme

France
France Genomique: training

Germany
Mediathek Humangenetik
First German Academy for Further Medical Training on Rare Diseases (FAKSE)

Scotland
Scottish Genetics Education Network (ScotGEN)
Scottish Genomes Partnership (see Patients & Families)