HGVS Nomenclature and Variant Classification Flashcards
Sample Variant Classification System
- Pathogenic (Positive)
- Variant, Expected Pathogenic
- Variant of Unknown Significance
- Variant, Likely Benign
- Benign or Polymorphism (Negative)
International Agency for Research on Cancer Classification
Class: 5; Definitely pathogenic; Clinical testing = Test at-risk relatives for the variant; Surveillance recommendations: Full high-risk surveillance
Class: 4; Likely pathogenic; Clinical testing = test at-risk relatives for the variant; Surveillance recommendations: Full high-risk surveillance
Class: 3; Uncertain; Clinical testing = do not use as predictive testing in at-risk relatives; Surveillance recommendations: Counsel based on family history and other risk factors
Class: 2; Likely not pathogenic; Clinical testing = do not use predictive testing in at-risk relatives; Surveillance recommendations: counsel as if no mutation detected
Class: 1; Not pathogenic
HGVS Intronic Nucleotide numbering
- Beginning of the intron: number of the last nucleotide of the preceding exon, a plus sign, and the position in the intron, like c.77+1G, c.77+2T, etc.
- Middle of the intron: numbering changes from “c.77+..” to “c.78-..”; for introns with an uneven number of nucleotides the central nucleotide is the last described with a “+”
- End of the intron: the number of the first nucleotide of the following exon, a minus sign, and the position upstream in the intron, like c.78-1G
Nonsense Mutation
- Replacement of a single nucleotide: incorrect sequence causes shortening of protein
Missense Mutation
- Replacement of a single nucleotide: incorrect amino acid, which may produce a malfunctioning protein
Insertion Mutation
- In a duplication, these inserted base pairs exactly match the adjacent DNA (ie. the same preceding nucleotides)
Frameshift Mutation
- Frameshift of one DNA base results in abnormal amino acid sequence
Deletion Mutation
- Deletion of a single nucleotide
Canonical Splice Site Mutations
- Donor site is always GT and denoted with a (+1, +2) e.g. IVS+1G>
- Acceptor site is always AG and denoted with a (-1,-2) e.g. IVS6-1A>C
Other splicing variants
- other consensus sequence elements in the intron may also impact splicing
- Also exonic variants may be splicing enhancers or cryptic splice sites
How are Variants classified? (IMPORTANT)
- Does the variant/alteration disrupt the gene function?
- Does the variant/alteration lead to disease?
- Is this variant causative of my patient’s presentation?
Frequency of the variant in general population
- Is it a known polymorphism/benign variant?
- Does it have a high frequency in the population? - Yes? Points towards benign; No? Points towards pathogenic
Population Frequency Example
- MYBPC3 gene (associated with HCM) - 1.4% MAF in AA
- HCM is ~1/500 (0.2%)
- Variant is far too common to be causative of Mendelian disease
Population frequency: common traps
- Not all populations are well-covered
- Reduced penetrance: may allow variant to exist at a higher frequency than expected due to less selective pressure
- Recessive variants may be present at a high frequency: Example: CFTR ChangeF508 (CF carrier rate = ~1/20 in the Caucasian population)
- Variant may be frequen in certain ethnic or geographic population - Example: BRCA1 - common Ashkenazi Jew mutation
- How different is the wild-type amino acid from the newly changed amino acid?
- Non conservative: different properties (points to pathogenic)
- Semi-Conservative = similar shape, other properties different
- Conservative = similar properties (points to benign)
