DNA Variant Card'

HGVS nomenlature summary and simple examples.
The HGVS (Human Genome Variation Society) is an internationally-recognized standard for the description of DNA, RNA, and protein sequence variants. It is used to convey variants in clinical reports and to share variants in publications and databases.

HGVS format:

sequence_identifier ':' coordinate_type '.' variant_definition 
example   NM_23456   :         c         .     A>C

(NM_23456:c.A>C)
- sequence_identifier: NM_xx , NP_xx , etc.
- coordinate_type is 'c' if transript sequence, is 'g' if genomic sequence, is 'p' if proteic sequence
- variant_definition see table below

For further information see HGVS Syntax Summary from HGVS Nomenclature

To help the user, the program, also accepts incorrect HGVS format. If it can unambiguously interpret the user's intention, it rewrites the variants in the correct HGVS format (see below).

Variant type	variant_definition example	..seq_reference.. ..seq_variant..	Note
Substitution	.45A>C	..acctActtgc.. ..acctCcttgc..	substitutions involving two or more consecutive nucleotides are described as deletion/insertion (delins) variants Our program also accepts c.45AC>GT. The program checks if the reference sequence is correct and then rewrites in the correct HGVS format (c.45_46delinsGT)
Deletion	.45del (only one nucleotide) .45_47del (more nucleotide)	..acctACTgcta.. ..acct...gcta..	Our program also accepts .45_47delACT (In this case checks if the reference sequence is correct)
Duplication	.55dup (only one nucleotide) .55_57dup (more nucleotide)	..tgcaCTTacga.. ..tgcaCTTCTTacga..	The program accepts, for example, also 55_56insCTT. If the three previous bases (53_55), in the reference sequence, are CTT, then it rewrites the variant in the correct HGVS format (.55_57dup)
Insertion	.45_46insACT	45\| \|46 ..cgta...cgaa.. ..cgtaACTcgaa..	Insert ACT from 45 to 46 nucleotide position
Inversion	.66_68inv	..cgtaATTctgg.. ..cgtaTTActgg..	In this case, the variation would correspond to .66_68delinsTTA. The program accepts this form, check the reference sequence, and then rewrites it into the correct HGVS format (.66_68inv)
Deletion-Insertion	60delinsACT .60_62delinsGG	..cgtaACTgcca.. ..cgtaGG.gcca..	Our program also accepts .60_62delACTinsGG (In this case checks if the reference sequence is correct)