Variants Mapping

Question 1

Minor Allele Frequency (MAF)

Answer 1

The frequency at which the second-most common allele at that position occurs. Generally more informative than allele frequency as it shows the mutability of that position.

Question 2

Genome Aggregation Database - gnomAD

Answer 2

• Formerly Exome Aggregation Consortium (ExAC)
• Maintained by Broad Institute
• Two short variant databases: gnomAD v2 and gnomAD v3
• Includes 1KGP and ClinVar data

Question 3

Pathogenic Variant Databases

Answer 3

• Variants that are associated with disease or pathology may not be found in general population studies, especially if high penetrance
• Important to record disease-associated variants and the evidence for this classification
• Also important to identify genes, domains, specific positions that can be consistently associated with the same conditions
• Numerous databases developed and curated to help individuals find and record variants that are thought to cause or modulate disease

Question 4

ClinVar

Answer 4

Reported pathogenic variants are mapped to reference sequences and interpreted by curators

Question 5

Online Mendelian Inheritance in Man

Answer 5

• Online catalogue of human genes and phenotypes associated with genetic variants
• Only selected variants are included
• Each variant is summarised with the evidence for inclusion
• Useful for linking genes, phenotypes, and most noteworthy variants

Question 6

Catalogue of Somatic Mutations in Cancer

Answer 6

• Curated database of somatic mutations linked to cancer
• View the distribution of variants across protein sequences, genes, and tissues
• Links to external resources