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HGVS Syntax Summary#

variant type molecule type forms, syntax, and examples
sub dna Simple sequence substitution
sequence_identifier ":" coordinate_type "." position reference_sequence ">" alternate_sequence
NC_000023.10:g.33038255C>A
Genome reference with coordinates from aligned transcript
sequence_identifier "(" transcript_identifier "):c." transcript_position reference_sequence ">" alternate_sequence
NG_012232.1(NM_004006.2):c.93+1G>T
rna sequence_identifier ":" coordinate_type "." position reference_nucleotide ">" new_nucleotide
NM_004006.3:r.123c>g
aa Experimentally ascertained protein consequence
sequence_identifier ":" coordinate_type "." aa_position alternate_base
NP_003997.1:p.Trp24Cys
NP_003997.1:p.Trp24Ter
NP_003997.1:p.W24*
Predicted protein consequence
sequence_identifier ":" coordinate_type "." "(" aa_position alternate_base ")"
NP_003997.1:p.(Trp24Cys)
del dna sequence_identifier ":" coordinate_type "." position_or_range "del"
NC_000001.11:g.1234del
NC_000001.11:g.1234_2345del
rna sequence_identifier ":" coordinate_type "." position "del"
NM_004006.3:r.123_127del
aa Single position
sequence_identifier ":" coordinate_type "." aa_position "del"
NP_003997.2:p.Val7del
Position range
sequence_identifier ":" coordinate_type "." aa_position "_" aa_position "del"
NP_003997.2:p.Lys23_Val25del
Alternative view
sequence_identifier ":" coordinate_type "." aa_range "del"
NP_003997.2:p.Lys23_Val25del
ins dna sequence_identifier ":" coordinate_type "." range "ins" sequence
NC_000001.11:g.1234_1235insACGT
rna sequence_identifier ":" coordinate_type "." positions "ins" sequence
NM_004006.3:r.123_124insauc
aa sequence_identifier ":" coordinate_type "." aa_range "ins" sequence
NP_004371.2:p.(Pro46_Asn47insSerSerTer)
delins dna single position
sequence_identifier ":" coordinate_type "." position "delins" sequence
NC_000001.11:g.123delinsAC
position range
sequence_identifier ":" coordinate_type "." range "delins" sequence
NC_000001.11:g.123_129delinsAC
rna sequence_identifier ":" coordinate_type "." position "delins" sequence
NM_004006.3:r.123_127delinsag
aa single position
sequence_identifier ":" coordinate_type "." aa_position "delins" sequence
NP_004371.2:p.Asn47delinsSerSerTer
NP_004371.2:p.(Asn47delinsSerSerTer)
position range
sequence_identifier ":" coordinate_type "." aa_position "_" aa_position "delins" sequence
NP_003070.3:p.Glu125_Ala132delinsGlyLeuHisArgPheIleValLeu
dup dna sequence_identifier ":" coordinate_type "." position_or_range "dup"
NC_000001.11:g.1234dup
NC_000001.11:g.1234_2345dup
rna sequence_identifier ":" coordinate_type "." position "dup"
NM_004006.3:r.123_345dup
aa single position
sequence_identifier ":" coordinate_type "." aa_position "dup"
NP_003997.2:p.Val7dup
position range
sequence_identifier ":" coordinate_type "." aa_position "_" aa_position "delins" sequence
NP_003997.2:p.Lys23_Val25dup
inv dna sequence_identifier ":" coordinate_type "." range "inv"
NC_000001.11:g.1234_2345inv
rna sequence_identifier ":" coordinate_type "." positions "inv"
NM_004006.3:r.123_345inv
rpt dna Unique Repeat
sequence_identifier ":" coordinate_type "." position sequence "[" total_copy_number "]"
NC_000014.8:g.123CAG[23]
Mixed Repeat
sequence_identifier ":" coordinate_type "." position sequence "[" total_copy_number "]" sequence "[" total_copy_number "]" … sequence "[" total_copy_number "]"
NC_000014.8:g.123_191CAG[19]CAA[4]
rna Positions only
sequence_identifier ":" coordinate_type "." positions "[" copy_number "]"
NM_004006.3:r.9495_9497[4]
NM_004006.3:r.-110_-108[6]
Sequence given
sequence_identifier ":" coordinate_type "." start_position sequence "[" copy_number "]"
NM_004006.3:r.9495caa[4]
NM_004006.3:r.-110gcu[6]
aa sequence_identifier ":" coordinate_type "." position sequence "[" total_copy_number "]"
NP_01234.5:p.Ala2[10]
NP_01234.5:p.Ala2[10];[11]
NP_01234.5:p.Arg65_Ser67[12]
alleles dna Variants in cis
sequence_identifier ":" coordinate_type "." "[" position_edit ";" position_edit "]"
NC_000001.11:g.[123G>A;345del]
Variants in trans
sequence_identifier ":" coordinate_type "." "[" position_edit "]" ";" "[" position_edit "]"
NC_000001.11:g.[123G>A];[345del]
Variants with unknown or uncertain phase
sequence_identifier ":" coordinate_type "." position_edit "(;)" position_edit
NC_000001.11:g.123G>A(;)345del
rna Variants in cis
sequence_identifier ":" coordinate_type "." "[" first_change ";" second_change "]"
NM_004006.3:r.[123c>a;345del]
Variants in trans
sequence_identifier ":" coordinate_type "." "[" first_change "]" ";" "[" second_change "]"
NM_004006.3:r.[123c>a];[345del]
Variants with unknown or uncertain phase
sequence_identifier ":" coordinate_type "." first_change "(;)" second_change
NM_004006.3:r.123c>a(;)345del
aa Variants in cis
sequence_identifier ":" coordinate_type "." "[" position_edit ";" position_edit "]"
NP_003997.1:p.[(Ser73Arg;Asn103del)]
Variants in trans
sequence_identifier ":" coordinate_type "." "[" position_edit "]" ";" "[" position_edit "]"
NP_003997.1:p.[(Ser73Arg)];[(Asn103del)]
Variants with unknown or uncertain phase
sequence_identifier ":" coordinate_type "." position_edit "(;)" position_edit
NP_003997.1:p.(Ser73Arg)](;)[(Asn103del)
ext aa N-terminus extension
sequence_identifier ":" coordinate_type "." "Met1" "ext" new_initiation_site
NP_003997.2:p.Met1ext-5
C-terminus extension
sequence_identifier ":" coordinate_type "." "Ter" aa_position aa "ext" "Ter" extension_length
NP_003997.2:p.Ter110GlnextTer17
fs aa Long format when stop codon position is known
sequence_identifier ":" coordinate_type "." aa_position "fs" [ "Ter" position ]
NP_01234.5:p.Arg97ProfsTer23
NP_01234.5:p.Arg97fs
other dna sequence_identifier ":" coordinate_type "." position_or_range "="
NC_000001.11:g.1234=
NC_000001.11:g.1234_2345=