Lecture 17: HGVS Reporting of Sequence Variations

These flashcards cover key concepts from the lecture on HGVS reporting of sequence variations, focusing on terminology, definitions, and reporting guidelines.

HGVS Nomenclature

An internationally-recognized standard for the description of DNA, RNA, and protein sequence variants.

Mutation

A change in the DNA sequence that may lead to disease; often avoided in the context of variant reporting.

Polymorphism

A non-disease-causing change in the genome that occurs at a frequency of 1% or higher.

De novo somatic variants

Additional changes in the cancer tissue that are called mutations.

Reference sequence

A unique identifier for a given DNA, RNA, or protein sequence used for reporting variants.

Amino acid abbreviation for Methionine

Denoted as the first amino acid for numbering, often represented as 'Met' or 'M'.

Protein termination notation

Reported as 'Ter' or '*' in protein sequence, indicating the end of the amino acid sequence.

Insertion reporting format

Reported using the format 'c.51_52insT', specifying the inserted sequence.

The 3' rule

For deletions, duplications, and insertions, the most 3' position changes are assigned arbitrarily.

Transversion

A type of nucleotide substitution where a purine is replaced by a pyrimidine or vice versa.

Neutral terminology in genetics

Terms like variant, alteration, or change that avoid the implications of 'mutation' or 'polymorphism'.

Checklist for reporting variants

A list ensuring correct application of HGVS nomenclature rules, such as reference sequence identification.