public enum VariantEffect extends Enum<VariantEffect>
Enum Constant and Description |
---|
_SMALLEST_HIGH_IMPACT
Marker for smallest
VariantEffect with PutativeImpact.HIGH impact. |
_SMALLEST_LOW_IMPACT
Marker for smallest
VariantEffect with PutativeImpact.LOW impact. |
_SMALLEST_MODERATE_IMPACT
Marker for smallest
VariantEffect with PutativeImpact.MODERATE impact. |
CHROMOSOME
SO:0000340 Structural unit
composed of a nucleic acid molecule which controls its own replication through the interaction of specific
proteins at one or more origins of replication (is a: replicon).
|
CHROMOSOME_NUMBER_VARIATION
SO:1000182 A kind of chromosome
variation where the chromosome complement is not an exact multiple of the haploid number (is a
chromosome_variation).
|
CODING_SEQUENCE_VARIANT
SO:0001580 A sequence variant
that changes the coding sequence (is a:
CODING_TRANSCRIPT_VARIANT , EXON_VARIANT ). |
CODING_TRANSCRIPT_INTRON_VARIANT
SO:0001969 A sequence variant
that changes non-coding intro sequence in a non-coding transcript (is a:
CODING_TRANSCRIPT_VARIANT ,
INTRON_VARIANT ). |
CODING_TRANSCRIPT_VARIANT
SO:0001968 A transcript variant
of a protein coding gene (is a:
TRANSCRIPT_VARIANT ). |
COMPLEX_SUBSTITUTION
SO:1000005 When no simple or
well defined DNA mutation event describes the observed DNA change, the keyword "complex" should be used.
|
CONSERVED_INTERGENIC_VARIANT
SO:0002017 A sequence variant
located in a conserved intergenic region, between genes (is a:
INTERGENIC_VARIANT ). |
CONSERVED_INTRON_VARIANT
SO:0002018 A transcript variant
occurring within a conserved region of an intron (is a:
INTRON_VARIANT ). |
CUSTOM
Variant in a user-specified custom region.
|
DIRECT_TANDEM_DUPLICATION
SO:1000039 A tandem duplication
where the individual regions are in the same orientation (is a: tandem_duplication).
|
DISRUPTIVE_INFRAME_DELETION
SO:0001826 An inframe decrease
in cds length that deletes bases from the coding sequence starting within an existing codon (is a:
INFRAME_DELETION ). |
DISRUPTIVE_INFRAME_INSERTION
SO:0001824 An inframe increase
in cds length that inserts one or more codons into the coding sequence within an existing codon (is a:
INFRAME_INSERTION ). |
DOWNSTREAM_GENE_VARIANT
SO:0001632 A sequence variant
located 3' of a gene (is a:
INTERGENIC_VARIANT ). |
EXON_LOSS_VARIANT
SO:0001572 A sequence variant
whereby an exon is lost from the transcript (is a (is a:
SPLICING_VARIANT ), TRANSCRIPT_VARIANT
). |
EXON_VARIANT
SO:0001791 A sequence variant
that changes exon sequence (is a:
TRANSCRIPT_VARIANT ). |
FEATURE_TRUNCATION
SO:0001906 A sequence variant
that causes the reduction of a genomic feature, with regard to the reference sequence (is a: feature_variant).
|
FIVE_PRIME_UTR_EXON_VARIANT
SO:0002092 A UTR variant of the
5' UTR (is a: 5_prime_UTR_variant; is a: UTR_variant).
|
FIVE_PRIME_UTR_INTRON_VARIANT
SO:0002091 A UTR variant
between 5' UTRs (is a: 5_prime_UTR_variant; is a: UTR_variant).
|
FIVE_PRIME_UTR_PREMATURE_START_CODON_GAIN_VARIANT
SO:0001983 A 5' UTR variant
where a premature start codon is introduced, moved or lost (is a:
FIVE_PRIME_UTR_EXON_VARIANT or
FIVE_PRIME_UTR_INTRON_VARIANT ). |
FIVE_PRIME_UTR_TRUNCATION
SO:0002013 A sequence variant
that causes the reduction of a the 5'UTR with regard to the reference sequence (is a:
FIVE_PRIME_UTR_EXON_VARIANT or FIVE_PRIME_UTR_INTRON_VARIANT )
Jannovar does not yield use this at the moment. |
FRAMESHIFT_ELONGATION
SO:0001909 A frameshift variant
that causes the translational reading frame to be extended relative to the reference feature (is a
FRAMESHIFT_VARIANT , internal_feature_elongation). |
FRAMESHIFT_TRUNCATION
SO:0001910 A frameshift variant
that causes the translational reading frame to be shortened relative to the reference feature (is a
FRAMESHIFT_VARIANT , internal_feature_truncation). |
FRAMESHIFT_VARIANT
SO:0001589A sequence variant
which causes a disruption of the translational reading frame, because the number of nucleotides inserted or
deleted is not a multiple of threee (is a: protein_altering_variant).
|
GENE_VARIANT
SO:0001564 A sequence variant
where the structure of the gene is changed (is a: feature_variant).
|
INFRAME_DELETION
SO:0001822 An inframe non
synonymous variant that deletes bases from the coding sequence (is a: inframe_indel, feature_truncation).
|
INFRAME_INSERTION
SO:0001821 An inframe non
synonymous variant that inserts bases into in the coding sequence (is a: inframe_indel,
internal_feature_elongation).
|
INITIATOR_CODON_VARIANT
SO:0001582 A codon variant that
changes at least one base of the first codon of a transcript (is a:
CODING_SEQUENCE_VARIANT , children:
start_retained_variant, start_lost). |
INTERGENIC_REGION
SO:0000605 A region containing
or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the
chromosome (is a: biological_region).
|
INTERGENIC_VARIANT
SO:0001628 A sequence variant
located in the intergenic region, between genes (is a: feature_variant).
|
INTERNAL_FEATURE_ELONGATION
SO:0001908 A sequence variant
that causes the extension of a genomic feature from within the feature rather than from the terminus of the
feature, with regard to the reference sequence.
|
INTRAGENIC_VARIANT
SO:0002011 A variant that
occurs within a gene but falls outside of all transcript features.
|
INTRON_VARIANT
SO:0001627 A transcript variant
occurring within an intron (is a:
TRANSCRIPT_VARIANT ). |
MIRNA
SO:0000276 Variant affects a
miRNA (is a: miRNA_primary_transcript, small_regulatory_ncRNA).
|
MISSENSE_VARIANT
SO:0001583 A sequence variant,
that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved.
|
MNV
SO:0002007 An MNV is a multiple
nucleotide variant (substitution) in which the inserted sequence is the same length as the replaced sequence (is
a: substitution).
|
NON_CODING_TRANSCRIPT_EXON_VARIANT
SO:0001792 A sequence variant
that changes non-coding exon sequence in a non-coding transcript (is a:
NON_CODING_TRANSCRIPT_VARIANT ,
EXON_VARIANT ). |
NON_CODING_TRANSCRIPT_INTRON_VARIANT
SO:0001970 A sequence variant
that changes non-coding intro sequence in a non-coding transcript (is a:
NON_CODING_TRANSCRIPT_VARIANT ,
INTRON_VARIANT ). |
NON_CODING_TRANSCRIPT_VARIANT
SO:0001619 (is a:
TRANSCRIPT_VARIANT ). |
RARE_AMINO_ACID_VARIANT
SO:0002008 A sequence variant
whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded
amino acid (children: selenocysteine_loss, pyrrolysine_loss).
|
REGULATORY_REGION_VARIANT
SO:0001566 A sequence variant
located within a regulatory region (is a: feature_variant).
|
SEQUENCE_VARIANT
SO:0001060 Top level term for
variants, can be used for marking "uknown effect".
|
SPLICE_ACCEPTOR_VARIANT
SO:0001574 A splice variant
that changes the 2 base region at the 3' end of an intron (is a
SPLICE_REGION_VARIANT ). |
SPLICE_DONOR_VARIANT
SO:0001575 A splice variant
that changes the 2 base pair region at the 5' end of an intron (is a
SPLICE_REGION_VARIANT ). |
SPLICE_REGION_VARIANT
SO:0001630 A sequence variant
in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8
bases of the intron (is a:
SPLICING_VARIANT ). |
SPLICING_VARIANT
SO:0001568 A sequence variant
that changes the process of splicing (is a:
GENE_VARIANT ). |
START_LOST
SO:0002012 A codon variant that
changes at least one base of the canonical start codon (is a: initiator_codon_variant).
|
STOP_GAINED
SO:0001587 A sequence variant
whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened
transcript (is a: nonsynonymous_variant, feature_truncation).
|
STOP_LOST
SO:0001578 A sequence variant
where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (is a:
nonsynonymous variant, terminator_codon_variant, feature_elongation)
|
STOP_RETAINED_VARIANT
SO:0001567 A sequence variant
where at least one base in the terminator codon is changed, but the terminator remains (is a:
SYNONYMOUS_VARIANT , terminator_codon_variant). |
STRUCTURAL_VARIANT
SO:0001537 A sequence variant
that changes one or more sequence features (is a: sequence variant).
|
SYNONYMOUS_VARIANT
SO:0001819 A sequence variant
where there is no resulting change to the encoded amino acid (is a:
CODING_SEQUENCE_VARIANT , children:
start_retained_variant, stop_retained_variant). |
TF_BINDING_SITE_VARIANT
SO:0001782 A sequence variant
located within a transcription factor binding site (is a:
REGULATORY_REGION_VARIANT ). |
THREE_PRIME_UTR_EXON_VARIANT
SO:0002089 A UTR variant of the
3' UTR (is a: 3_prime_UTR_variant; is a: UTR_variant).
|
THREE_PRIME_UTR_INTRON_VARIANT
SO:0002090 A UTR variant
between 3' UTRs (is a: 3_prime_UTR_variant; is a: UTR_variant).
|
THREE_PRIME_UTR_TRUNCATION
SO:0002015 A sequence variant
that causes the reduction of a the 3' UTR with regard to the reference sequence (is a:
FIVE_PRIME_UTR_EXON_VARIANT or FIVE_PRIME_UTR_INTRON_VARIANT ). |
TRANSCRIPT_ABLATION
SO:0001893 A feature ablation
whereby the deleted region includes a transcript feature (is a: feature_ablation)
Not used in Jannovar annotations.
|
TRANSCRIPT_VARIANT
SO:0001576 A sequence variant
that changes the structure of the transcript (is a:
GENE_VARIANT ). |
UPSTREAM_GENE_VARIANT
SO:0001631 A sequence variant
located 5' of a gene (is a:
INTERGENIC_VARIANT ). |
Modifier and Type | Field and Description |
---|---|
static com.google.common.base.Predicate<VariantEffect> |
IS_INTRONIC
Predicate for testing whether a VariantEffect is intronic. |
static com.google.common.base.Predicate<VariantEffect> |
IS_SPLICING
Predicate for testing whether a VariantEffect is related to splicing. |
static com.google.common.base.Function<VariantEffect,String> |
TO_LEGACY_NAME
Function for converting from VariantEffect to legacy term. |
static com.google.common.base.Function<VariantEffect,String> |
TO_SO_TERM
Function for converting from VariantEffect to SO term String. |
Modifier and Type | Method and Description |
---|---|
PutativeImpact |
getImpact() |
String |
getLegacyTerm() |
int |
getNumber()
Forward to
ordinal() member function. |
String |
getSequenceOID() |
String |
getSequenceOntologyTerm() |
boolean |
isIntronic() |
boolean |
isOffExome() |
boolean |
isOffTranscript() |
boolean |
isSplicing() |
boolean |
isStructural() |
static VariantEffect |
valueOf(String name)
Returns the enum constant of this type with the specified name.
|
static VariantEffect[] |
values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
public static final VariantEffect CHROMOSOME_NUMBER_VARIATION
public static final VariantEffect TRANSCRIPT_ABLATION
public static final VariantEffect EXON_LOSS_VARIANT
SPLICING_VARIANT
), TRANSCRIPT_VARIANT
).
Not used in Jannovar annotations.public static final VariantEffect FRAMESHIFT_ELONGATION
FRAMESHIFT_VARIANT
, internal_feature_elongation).public static final VariantEffect FRAMESHIFT_TRUNCATION
FRAMESHIFT_VARIANT
, internal_feature_truncation).public static final VariantEffect FRAMESHIFT_VARIANT
public static final VariantEffect INTERNAL_FEATURE_ELONGATION
COMPLEX_SUBSTITUTION
that does not lead to a frameshift and increases
the transcript length.public static final VariantEffect FEATURE_TRUNCATION
COMPLEX_SUBSTITUTION
that does not lead to a frameshift and decreases
the transcript length.public static final VariantEffect MNV
public static final VariantEffect COMPLEX_SUBSTITUTION
INTERNAL_FEATURE_ELONGATION
or FEATURE_TRUNCATION
to describe an variant
that does not lead to a frameshift but a changed transcript length. Used together with
FRAMESHIFT_ELONGATION
or FRAMESHIFT_TRUNCATION
if the substitution leads to a frameshift
variant.public static final VariantEffect STOP_GAINED
public static final VariantEffect STOP_LOST
public static final VariantEffect START_LOST
public static final VariantEffect SPLICE_ACCEPTOR_VARIANT
SPLICE_REGION_VARIANT
).public static final VariantEffect SPLICE_DONOR_VARIANT
SPLICE_REGION_VARIANT
).public static final VariantEffect RARE_AMINO_ACID_VARIANT
public static final VariantEffect _SMALLEST_HIGH_IMPACT
VariantEffect
with PutativeImpact.HIGH
impact.public static final VariantEffect MISSENSE_VARIANT
public static final VariantEffect INFRAME_INSERTION
public static final VariantEffect DISRUPTIVE_INFRAME_INSERTION
INFRAME_INSERTION
).public static final VariantEffect INFRAME_DELETION
public static final VariantEffect DISRUPTIVE_INFRAME_DELETION
INFRAME_DELETION
).public static final VariantEffect FIVE_PRIME_UTR_TRUNCATION
FIVE_PRIME_UTR_EXON_VARIANT
or FIVE_PRIME_UTR_INTRON_VARIANT
)
Jannovar does not yield use this at the moment.public static final VariantEffect THREE_PRIME_UTR_TRUNCATION
FIVE_PRIME_UTR_EXON_VARIANT
or FIVE_PRIME_UTR_INTRON_VARIANT
).
Jannovar does not yield use this at the moment.public static final VariantEffect SPLICE_REGION_VARIANT
SPLICING_VARIANT
).public static final VariantEffect _SMALLEST_MODERATE_IMPACT
VariantEffect
with PutativeImpact.MODERATE
impact.public static final VariantEffect STOP_RETAINED_VARIANT
SYNONYMOUS_VARIANT
, terminator_codon_variant).public static final VariantEffect INITIATOR_CODON_VARIANT
CODING_SEQUENCE_VARIANT
, children:
start_retained_variant, start_lost).public static final VariantEffect SYNONYMOUS_VARIANT
CODING_SEQUENCE_VARIANT
, children:
start_retained_variant, stop_retained_variant).public static final VariantEffect CODING_TRANSCRIPT_INTRON_VARIANT
CODING_TRANSCRIPT_VARIANT
,
INTRON_VARIANT
).public static final VariantEffect NON_CODING_TRANSCRIPT_EXON_VARIANT
NON_CODING_TRANSCRIPT_VARIANT
,
EXON_VARIANT
).public static final VariantEffect NON_CODING_TRANSCRIPT_INTRON_VARIANT
NON_CODING_TRANSCRIPT_VARIANT
,
INTRON_VARIANT
).public static final VariantEffect FIVE_PRIME_UTR_PREMATURE_START_CODON_GAIN_VARIANT
FIVE_PRIME_UTR_EXON_VARIANT
or
FIVE_PRIME_UTR_INTRON_VARIANT
).
Not used in Jannovar annotations.public static final VariantEffect FIVE_PRIME_UTR_EXON_VARIANT
public static final VariantEffect THREE_PRIME_UTR_EXON_VARIANT
public static final VariantEffect FIVE_PRIME_UTR_INTRON_VARIANT
public static final VariantEffect THREE_PRIME_UTR_INTRON_VARIANT
public static final VariantEffect _SMALLEST_LOW_IMPACT
VariantEffect
with PutativeImpact.LOW
impact.public static final VariantEffect DIRECT_TANDEM_DUPLICATION
public static final VariantEffect CUSTOM
public static final VariantEffect UPSTREAM_GENE_VARIANT
INTERGENIC_VARIANT
).public static final VariantEffect DOWNSTREAM_GENE_VARIANT
INTERGENIC_VARIANT
).public static final VariantEffect INTERGENIC_VARIANT
public static final VariantEffect TF_BINDING_SITE_VARIANT
REGULATORY_REGION_VARIANT
).
Not used in Jannovar annotations.public static final VariantEffect REGULATORY_REGION_VARIANT
public static final VariantEffect CONSERVED_INTRON_VARIANT
INTRON_VARIANT
).
Not used in Jannovar annotations.public static final VariantEffect INTRAGENIC_VARIANT
TRANSCRIPT_VARIANT
).public static final VariantEffect CONSERVED_INTERGENIC_VARIANT
INTERGENIC_VARIANT
).public static final VariantEffect STRUCTURAL_VARIANT
public static final VariantEffect CODING_SEQUENCE_VARIANT
CODING_TRANSCRIPT_VARIANT
, EXON_VARIANT
).
Sequence Ontology does not have a term
CODING_TRANSCRIPT_EXON_VARIANT, so we use this.
Not used in Jannovar annotations.public static final VariantEffect INTRON_VARIANT
TRANSCRIPT_VARIANT
).
Jannovar uses CODING_TRANSCRIPT_INTRON_VARIANT
and NON_CODING_TRANSCRIPT_INTRON_VARIANT
instead.public static final VariantEffect EXON_VARIANT
TRANSCRIPT_VARIANT
).public static final VariantEffect SPLICING_VARIANT
GENE_VARIANT
).
Not used in Jannovar annotations.public static final VariantEffect MIRNA
public static final VariantEffect GENE_VARIANT
public static final VariantEffect CODING_TRANSCRIPT_VARIANT
TRANSCRIPT_VARIANT
).
Not used in Jannovar annotations.public static final VariantEffect NON_CODING_TRANSCRIPT_VARIANT
TRANSCRIPT_VARIANT
).
Used for marking splicing variants as non-coding.public static final VariantEffect TRANSCRIPT_VARIANT
GENE_VARIANT
). TRANSCRIPT_VARIANT, /**
SO: (is a: GENE_VARIANT
)).
Not used in Jannovar annotations.public static final VariantEffect INTERGENIC_REGION
public static final VariantEffect CHROMOSOME
public static final VariantEffect SEQUENCE_VARIANT
public static final com.google.common.base.Predicate<VariantEffect> IS_SPLICING
Predicate
for testing whether a VariantEffect
is related to splicing.public static final com.google.common.base.Predicate<VariantEffect> IS_INTRONIC
Predicate
for testing whether a VariantEffect
is intronic.public static final com.google.common.base.Function<VariantEffect,String> TO_SO_TERM
Function
for converting from VariantEffect
to SO term String.public static final com.google.common.base.Function<VariantEffect,String> TO_LEGACY_NAME
Function
for converting from VariantEffect
to legacy term.public static VariantEffect[] values()
for (VariantEffect c : VariantEffect.values()) System.out.println(c);
public static VariantEffect valueOf(String name)
name
- the name of the enum constant to be returned.IllegalArgumentException
- if this enum type has no constant with the specified nameNullPointerException
- if the argument is nullpublic String getLegacyTerm()
public PutativeImpact getImpact()
PutativeImpact
of this effect annotation.public String getSequenceOntologyTerm()
public int getNumber()
ordinal()
member function.int
with the number used for sorting values of type VariantEffect
.public boolean isStructural()
true
if this VariantEffect
annotates structural variants.public boolean isSplicing()
true
if this VariantEffect
could affect splicing.public boolean isIntronic()
true
if equal to CODING_TRANSCRIPT_INTRON_VARIANT
or
NON_CODING_TRANSCRIPT_INTRON_VARIANT
.public boolean isOffExome()
true
if the variant effect does not indicate a change affecting the exome, CUSTOM
is considered on-exomeisOffTranscript()
public boolean isOffTranscript()
true
if the variant effect does not indicate a change affecting a transcript,
CUSTOM
is considered on-transcriptisOffExome()
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