VariO type annotation examples

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Examples of use of VariO terms for annotation of variation types.
All these examples were generated using the VariO annotation tool VariOtator

DNA substitutions

substitution in 5' gene flanking region

NM_003990.3:c.-550C>T

c.-550C>T
VariO:0128 VariO variation affecting DNA
VariO:0129 DNA variation type
VariO:0322 DNA variation classification
VariO:0135 DNA chain variation
VariO:0136 DNA substitution
VariO:0313 transition
VariO:0314 pyrimidine transition


substitution in 5' UTR

NM_003990.3:c.-12C>A

c.-12C>A
VariO:0128 variation affecting DNA
VariO:0129 DNA variation type
VariO:0322 DNA variation classification
VariO:0135 DNA chain variation
VariO:0136 DNA substitution
VariO:0316 transversion


substitution in translation initiation codon

NM_003990.3:c.1A>C

c.1A>C
VariO:0128 variation affecting DNA
VariO:0129 DNA variation type
VariO:0322 DNA variation classification
VariO:0135 DNA chain variation
VariO:0136 DNA substitution
VariO:0316 transversion

r.(1a>c)
VariO:0297 variation affecting RNA
VariO:0306 RNA variation type
VariO:0328 RNA variation classification
VariO:0317 initiation codon change

VariO:0312 RNA substitution
VariO:0308 missense variation

VariO:0316 transversion


substitution in coding region

NM_003990.3:c.71G>A

c.71G>A
VariO:0128 variation affecting DNA
VariO:0129 DNA variation type
VariO:0322 DNA variation classification
VariO:0135 DNA chain variation
VariO:0136 DNA substitution
VariO:0313 transition
VariO:0315 purine transition

r.(71g>a)
VariO:0297 variation affecting RNA
VariO:0306 RNA variation type
VariO:0328 RNA variation classification
VariO:0312 RNA substitution
VariO:0315 purine transition

VariO:0308 missense variation

p.(Gly24Glu)
VariO:0002 variation affecting protein
VariO:0012 protein variation type
VariO:0325 protein variation classification
VariO:0021 amino acid substitution


substitution in 5' part intron

NG_008680.1:c.43+1G>C

c.43+1G>C
VariO:0128 variation affecting DNA
VariO:0129 DNA variation type
VariO:0322 DNA variation classification
VariO:0135 DNA chain variation
VariO:0136 DNA substitution
VariO:0316 transversion


substitution in 3' part intron

NG_008680.1:c.411-2A>G

c.411-2A>G
VariO:0128 variation affecting DNA
VariO:0129 DNA variation type
VariO:0322 DNA variation classification
VariO:0135 DNA chain variation
VariO:0136 DNA substitution
VariO:0313 transition
VariO:0315 purine transition


substitution in translation termination codon

NM_003990.3:c.1296A>G

c.1296A>G
VariO:0128 variation affecting DNA
VariO:0129 DNA variation type
VariO:0322 DNA variation classification
VariO:0135 DNA chain variation
VariO:0136 DNA substitution
VariO:0313 transition
VariO:0315 purine transition

r.(1296a>g)
VariO:0297 variation affecting RNA
VariO:0306 RNA variation type
VariO:0328 RNA variation classification
VariO:0312 RNA substitution
VariO:0313 transition
VariO:0315 purine transition

VariO:0309 termination codon change

p.(*432Trpext*144)
VariO:0002 variation affecting protein
VariO:0012 protein variation type
VariO:0325 protein variation classification
VariO:0022 amino acid indel
VariO:0023 amphigoric amino acid indel


substitution in 3' UTR

NM_003990.3:c.*70T>A

c.*70T>A
VariO:0128 variation affecting DNA
VariO:0129 DNA variation type
VariO:0322 DNA variation classification
VariO:0135 DNA chain variation
VariO:0136 DNA substitution
VariO:0316 transversion


substitution in 3' gene flanking region

NG_008680.1:c.*2280T>C

c.*2280T>C
VariO:0128 variation affecting DNA
VariO:0129 DNA variation type
VariO:0322 DNA variation classification
VariO:0135 DNA chain variation
VariO:0136 DNA substitution
VariO:0313 transition
VariO:0314 pyrimidine transition



DNA deletions

single nucleotide deletion

NM_003990.3:c.76del

c.76del
VariO:0128 variation affecting DNA
VariO:0129 DNA variation type
VariO:0322 DNA variation classification
VariO:0135 DNA chain variation
VariO:0141 DNA deletion

r.(76del)
VariO:0297 variation affecting RNA
VariO:0306 RNA variation type
VariO:0328 RNA variation classification
VariO:0319 RNA deletion
VariO:0321 out-of-frame deletion

p.(Val26Cysfs*3)
VariO:0002 variation affecting protein
VariO:0012 protein variation type
VariO:0325 protein variation classification
VariO:0022 amino acid indel
VariO:0023 amphigoric amino acid indel


several nucleotides deletion

coding region

NM_003990.3:c.92_97del

c.92_97del
VariO:0128 variation affecting DNA
VariO:0129 DNA variation type
VariO:0322 DNA variation classification
VariO:0135 DNA chain variation
VariO:0141 DNA deletion

r.(92_97del)
VariO:0297 variation affecting RNA
VariO:0306 RNA variation type
VariO:0328 RNA variation classification
VariO:0319 RNA deletion
VariO:0320 in-frame deletion

p.(Arg31_Pro32del)
VariO:0002 variation affecting protein
VariO:0012 protein variation type
VariO:0325 protein variation classification
VariO:0014 amino acid deletion
VariO:0016 sequence retaining amino acid deletion


deletion across exon 2/intron 3 border

NG_008680.1:c.120_212+48del

c.121_212+49del
VariO:0128 variation affecting DNA
VariO:0129 DNA variation type
VariO:0322 DNA variation classification
VariO:0135 DNA chain variation
VariO:0141 DNA deletion


(multi)exon deletion

breakpoints sequenced

NG_008680.1:c.44-10_411-30del

c.44-10_411-30del
VariO:0128 variation affecting DNA
VariO:0129 DNA variation type
VariO:0322 DNA variation classification
VariO:0135 DNA chain variation
VariO:0141 DNA deletion

p.(Pro15Glnfs*22)
VariO:0002 variation affecting protein
VariO:0012 protein variation type
VariO:0325 protein variation classification
VariO:0022 amino acid indel
VariO:0023 amphigoric amino acid indel


breakpoints not sequenced

NG_008680.1:c.213-?_496+?del

c.213-?_496+?del
VariO:0128 variation affecting DNA
VariO:0129 DNA variation type
VariO:0322 DNA variation classification
VariO:0135 DNA chain variation
VariO:0141 DNA deletion

p.(Arg71Serfs*15)
VariO:0002 variation affecting protein
VariO:0012 protein variation type
VariO:0325 protein variation classification
VariO:0022 amino acid indel
VariO:0023 amphigoric amino acid indel


DNA duplications

single nucleotide duplication

NM_003990.3:c.76dup

c.76dup
VariO:0128 variation affecting DNA
VariO:0129 DNA variation type
VariO:0322 DNA variation classification
VariO:0135 DNA chain variation
VariO:0142 DNA insertion

r.(76dup)
VariO:0297 variation affecting RNA
VariO:0306 RNA variation type
VariO:0328 RNA variation classification
VariO:0326 RNA insertion
VariO:0327 out-of-frame insertion

p.(Val26Glyfs*28)
VariO:0002 variation affecting protein
VariO:0012 protein variation type
VariO:0325 protein variation classification
VariO:0022 amino acid indel
VariO:0023 amphigoric amino acid indel


several nucleotides duplication

coding region

NM_003990.3:c.92_97dup

c.92_97dup
VariO:0128 variation affecting DNA
VariO:0129 DNA variation type
VariO:0322 DNA variation classification
VariO:0135 DNA chain variation
VariO:0142 DNA insertion

r.(92_97dup)
VariO:0297 variation affecting RNA
VariO:0306 RNA variation type
VariO:0328 RNA variation classification
VariO:0326 RNA insertion
VariO:0332 in-frame insertion

p.(Arg31_Pro32dup)
VariO:0002 variation affecting protein
VariO:0012 protein variation type
VariO:0325 protein variation classification
VariO:0018 amino acid insertion
VariO:0020 sequence retaining protein chain insertion


duplication across exon 2/intron 3 border

NG_008680.1:c.120_212+48dup

c.121_212+49dup
VariO:0128 variation affecting DNA
VariO:0129 DNA variation type
VariO:0322 DNA variation classification
VariO:0135 DNA chain variation
VariO:0142 DNA insertion


(multi)exon duplication

breakpoints sequenced

NG_008680.1:c.44-10_411-30dup

c.44-10_411-30dup
VariO:0128 variation affecting DNA
VariO:0129 DNA variation type
VariO:0322 DNA variation classification
VariO:0135 DNA chain variation
VariO:0142 DNA insertion


breakpoints not sequenced

NG_008680.1:c.44-?_410+?dup

c.44-?_410+?dup
VariO:0128 variation affecting DNA
VariO:0129 DNA variation type
VariO:0322 DNA variation classification
VariO:0135 DNA chain variation
VariO:0142 DNA insertion


DNA inversions

short inversion

NM_003990.3:c.72_75inv

c.72_75inv
VariO:0128 variation affecting DNA
VariO:0129 DNA variation type
VariO:0322 DNA variation classification
VariO:0135 DNA chain variation
VariO:0144 DNA translocation
VariO:0145 DNA inversion

r.(72_75inv)
VariO:0297 variation affecting RNA
VariO:0306 RNA variation type
VariO:0328 RNA variation classification
VariO:0241 RNA translocation
VariO:0244 RNA inversion

p.(Gly25Pro)
VariO:0002 variation affecting protein
VariO:0012 protein variation type
VariO:0325 protein variation classification
VariO:0021 amino acid substitution


several nucleotides insertion

NM_003990.3:c.92_93insGAG

c.93_94insAGG
VariO:0128 variation affecting DNA
VariO:0129 DNA variation type
VariO:0322 DNA variation classification
VariO:0135 DNA chain variation
VariO:0142 DNA insertion

r.(93_94insagg)
VariO:0297 variation affecting RNA
VariO:0306 RNA variation type
VariO:0328 RNA variation classification
VariO:0326 RNA insertion
VariO:0332 in-frame insertion

p.(Arg31dup)
VariO:0002 variation affecting protein
VariO:0012 protein variation type
VariO:0325 protein variation classification
VariO:0018 amino acid insertion
VariO:0020 sequence retaining protein chain insertion


insertion in intron

NG_006672.1:c.454+54_454+55insA

c.454+54_454+55insA
VariO:0128 variation affecting DNA
VariO:0129 DNA variation type
VariO:0322 DNA variation classification
VariO:0135 DNA chain variation
VariO:0142 DNA insertion


DNA indels

NM_001100.3:c.112_117delinsTG

c.112_117delinsTG
VariO:0128 variation affecting DNA
VariO:0129 DNA variation type
VariO:0322 DNA variation classification
VariO:0135 DNA chain variation
VariO:0143 DNA indel

r.(112_117delinsug)
VariO:0297 variation affecting RNA
VariO:0306 RNA variation type
VariO:0328 RNA variation classification
VariO:0311 RNA indel

p.(Gly38Cysfs*29)
VariO:0002 variation affecting protein
VariO:0012 protein variation type
VariO:0325 protein variation classification
VariO:0022 amino acid indel
VariO:0023 amphigoric amino acid indel


NM_001100.3:c.112_117delGGCCGCinsTG

c.112_117delinsTG
VariO:0128 variation affecting DNA
VariO:0129 DNA variation type
VariO:0322 DNA variation classification
VariO:0135 DNA chain variation
VariO:0143 DNA indel

r.(112_117delinsug)
VariO:0297 variation affecting RNA
VariO:0306 RNA variation type
VariO:0328 RNA variation classification
VariO:0311 RNA indel

p.(Gly38Cysfs*29)
VariO:0002 variation affecting protein
VariO:0012 protein variation type
VariO:0325 protein variation classification
VariO:0022 amino acid indel
VariO:0023 amphigoric amino acid indel


DNA translocation

t(X;4)(p21.2;q35)(c.301-148_300-147)

t(X;4)(p21.2;q35)(c.301-148_300-147)
VariO:0128 variation affecting DNA
VariO:0129 DNA variation type
VariO:0322 DNA variation classification
VariO:0135 DNA chain variation
VariO:0144 DNA translocation


The VariO ontology can be viewed using an ontology editor, such as OBO-Edit or the AmiVariO. AmiVariO is courtesy of AmiGO Gene Ontology browser. VariO is available in OBO, OWL and OWX formats at here.

VariO has been developed by Mauno Vihinen.