de.charite.compbio.jannovar.annotation

Enum VariantEffect

java.lang.Object

java.lang.Enum<VariantEffect>

de.charite.compbio.jannovar.annotation.VariantEffect

All Implemented Interfaces:

Serializable, Comparable<VariantEffect>

public enum VariantEffect
extends Enum<VariantEffect>

These codes reflect the possible types of variants that we call for an exome. The values in this enum are given in the putative order of impact (more severe to less severe). The documentation gives the sequence ontology (SO) ID and the SO description. Also, the documentation of each value explains whether Jannovar generates this annotation or not.

Author:

Peter Robinson, Marten Jaeger, Manuel Holtgrewe, Max Schubach

Enum Constant Summary

Enum Constants

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).

Field Summary

Fields

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.

Method Summary

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.

Methods inherited from class java.lang.Enum

compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

CHROMOSOME_NUMBER_VARIATION

public static final VariantEffect 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). Not used in Jannovar annotations.

TRANSCRIPT_ABLATION

public static final VariantEffect TRANSCRIPT_ABLATION

SO:0001893 A feature ablation whereby the deleted region includes a transcript feature (is a: feature_ablation) Not used in Jannovar annotations.

EXON_LOSS_VARIANT

public static final VariantEffect EXON_LOSS_VARIANT

SO:0001572 A sequence variant whereby an exon is lost from the transcript (is a (is a: SPLICING_VARIANT), TRANSCRIPT_VARIANT ). Not used in Jannovar annotations.

FRAMESHIFT_ELONGATION

public static final VariantEffect 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

public static final VariantEffect 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

public static final VariantEffect 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). Used for frameshift variant for the case where there is no stop codon any more and the rare case in which the transcript length is retained.

INTERNAL_FEATURE_ELONGATION

public static final VariantEffect 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. In Jannovar, used to annotate a COMPLEX_SUBSTITUTION that does not lead to a frameshift and increases the transcript length.

FEATURE_TRUNCATION

public static final VariantEffect 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). The term INTERNAL_FEATURE_TRUNCATION would be more fitting but is not available in SO. In Jannovar, used to annotate a COMPLEX_SUBSTITUTION that does not lead to a frameshift and decreases the transcript length.

MNV

public static final VariantEffect 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).

COMPLEX_SUBSTITUTION

public static final VariantEffect COMPLEX_SUBSTITUTION

SO:1000005 When no simple or well defined DNA mutation event describes the observed DNA change, the keyword "complex" should be used. Usually there are multiple equally plausible explanations for the change (is a: substitution). Used together with 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.

STOP_GAINED

public static final VariantEffect 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

public static final VariantEffect 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)

START_LOST

public static final VariantEffect START_LOST

SO:0002012 A codon variant that changes at least one base of the canonical start codon (is a: initiator_codon_variant).

SPLICE_ACCEPTOR_VARIANT

public static final VariantEffect 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

public static final VariantEffect 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).

RARE_AMINO_ACID_VARIANT

public static final VariantEffect 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). Not used in Jannovar annotations.

_SMALLEST_HIGH_IMPACT

public static final VariantEffect _SMALLEST_HIGH_IMPACT

Marker for smallest VariantEffect with PutativeImpact.HIGH impact.

MISSENSE_VARIANT

public static final VariantEffect 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.

INFRAME_INSERTION

public static final VariantEffect INFRAME_INSERTION

SO:0001821 An inframe non synonymous variant that inserts bases into in the coding sequence (is a: inframe_indel, internal_feature_elongation).

DISRUPTIVE_INFRAME_INSERTION

public static final VariantEffect 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).

INFRAME_DELETION

public static final VariantEffect INFRAME_DELETION

SO:0001822 An inframe non synonymous variant that deletes bases from the coding sequence (is a: inframe_indel, feature_truncation).

DISRUPTIVE_INFRAME_DELETION

public static final VariantEffect 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).

FIVE_PRIME_UTR_TRUNCATION

public static final VariantEffect 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.

THREE_PRIME_UTR_TRUNCATION

public static final VariantEffect 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). Jannovar does not yield use this at the moment.

SPLICE_REGION_VARIANT

public static final VariantEffect 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).

_SMALLEST_MODERATE_IMPACT

public static final VariantEffect _SMALLEST_MODERATE_IMPACT

Marker for smallest VariantEffect with PutativeImpact.MODERATE impact.

STOP_RETAINED_VARIANT

public static final VariantEffect 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).

INITIATOR_CODON_VARIANT

public static final VariantEffect 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).

SYNONYMOUS_VARIANT

public static final VariantEffect 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).

CODING_TRANSCRIPT_INTRON_VARIANT

public static final VariantEffect 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).

NON_CODING_TRANSCRIPT_EXON_VARIANT

public static final VariantEffect 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

public static final VariantEffect 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).

FIVE_PRIME_UTR_PREMATURE_START_CODON_GAIN_VARIANT

public static final VariantEffect 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). Not used in Jannovar annotations.

FIVE_PRIME_UTR_EXON_VARIANT

public static final VariantEffect FIVE_PRIME_UTR_EXON_VARIANT

SO:0002092 A UTR variant of the 5' UTR (is a: 5_prime_UTR_variant; is a: UTR_variant).

THREE_PRIME_UTR_EXON_VARIANT

public static final VariantEffect THREE_PRIME_UTR_EXON_VARIANT

SO:0002089 A UTR variant of the 3' UTR (is a: 3_prime_UTR_variant; is a: UTR_variant).

FIVE_PRIME_UTR_INTRON_VARIANT

public static final VariantEffect FIVE_PRIME_UTR_INTRON_VARIANT

SO:0002091 A UTR variant between 5' UTRs (is a: 5_prime_UTR_variant; is a: UTR_variant).

THREE_PRIME_UTR_INTRON_VARIANT

public static final VariantEffect THREE_PRIME_UTR_INTRON_VARIANT

SO:0002090 A UTR variant between 3' UTRs (is a: 3_prime_UTR_variant; is a: UTR_variant).

_SMALLEST_LOW_IMPACT

public static final VariantEffect _SMALLEST_LOW_IMPACT

Marker for smallest VariantEffect with PutativeImpact.LOW impact.

DIRECT_TANDEM_DUPLICATION

public static final VariantEffect DIRECT_TANDEM_DUPLICATION

SO:1000039 A tandem duplication where the individual regions are in the same orientation (is a: tandem_duplication). In Jannovar used, as an additional marker to describe that an insertion is a duplication.

CUSTOM

public static final VariantEffect CUSTOM

Variant in a user-specified custom region. Not used in Jannovar annotations.

UPSTREAM_GENE_VARIANT

public static final VariantEffect UPSTREAM_GENE_VARIANT

SO:0001631 A sequence variant located 5' of a gene (is a: INTERGENIC_VARIANT).

DOWNSTREAM_GENE_VARIANT

public static final VariantEffect DOWNSTREAM_GENE_VARIANT

SO:0001632 A sequence variant located 3' of a gene (is a: INTERGENIC_VARIANT).

INTERGENIC_VARIANT

public static final VariantEffect INTERGENIC_VARIANT

SO:0001628 A sequence variant located in the intergenic region, between genes (is a: feature_variant).

TF_BINDING_SITE_VARIANT

public static final VariantEffect TF_BINDING_SITE_VARIANT

SO:0001782 A sequence variant located within a transcription factor binding site (is a: REGULATORY_REGION_VARIANT). Not used in Jannovar annotations.

REGULATORY_REGION_VARIANT

public static final VariantEffect REGULATORY_REGION_VARIANT

SO:0001566 A sequence variant located within a regulatory region (is a: feature_variant). Not used in Jannovar annotations.

CONSERVED_INTRON_VARIANT

public static final VariantEffect CONSERVED_INTRON_VARIANT

SO:0002018 A transcript variant occurring within a conserved region of an intron (is a: INTRON_VARIANT). Not used in Jannovar annotations.

INTRAGENIC_VARIANT

public static final VariantEffect INTRAGENIC_VARIANT

SO:0002011 A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping sequence (is a: TRANSCRIPT_VARIANT ).

CONSERVED_INTERGENIC_VARIANT

public static final VariantEffect CONSERVED_INTERGENIC_VARIANT

SO:0002017 A sequence variant located in a conserved intergenic region, between genes (is a: INTERGENIC_VARIANT).

STRUCTURAL_VARIANT

public static final VariantEffect STRUCTURAL_VARIANT

SO:0001537 A sequence variant that changes one or more sequence features (is a: sequence variant).

CODING_SEQUENCE_VARIANT

public static final VariantEffect CODING_SEQUENCE_VARIANT

SO:0001580 A sequence variant that changes the coding sequence (is a: 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.

INTRON_VARIANT

public static final VariantEffect INTRON_VARIANT

SO:0001627 A transcript variant occurring within an intron (is a: TRANSCRIPT_VARIANT). Jannovar uses CODING_TRANSCRIPT_INTRON_VARIANT and NON_CODING_TRANSCRIPT_INTRON_VARIANT instead.

EXON_VARIANT

public static final VariantEffect EXON_VARIANT

SO:0001791 A sequence variant that changes exon sequence (is a: TRANSCRIPT_VARIANT).

SPLICING_VARIANT

public static final VariantEffect SPLICING_VARIANT

SO:0001568 A sequence variant that changes the process of splicing (is a: GENE_VARIANT). Not used in Jannovar annotations.

MIRNA

public static final VariantEffect MIRNA

SO:0000276 Variant affects a miRNA (is a: miRNA_primary_transcript, small_regulatory_ncRNA). Not used in Jannovar annotations.

GENE_VARIANT

public static final VariantEffect GENE_VARIANT

SO:0001564 A sequence variant where the structure of the gene is changed (is a: feature_variant). Not used in Jannovar annotations.

CODING_TRANSCRIPT_VARIANT

public static final VariantEffect CODING_TRANSCRIPT_VARIANT

SO:0001968 A transcript variant of a protein coding gene (is a: TRANSCRIPT_VARIANT). Not used in Jannovar annotations.

NON_CODING_TRANSCRIPT_VARIANT

public static final VariantEffect NON_CODING_TRANSCRIPT_VARIANT

SO:0001619 (is a: TRANSCRIPT_VARIANT). Used for marking splicing variants as non-coding.

TRANSCRIPT_VARIANT

public static final VariantEffect TRANSCRIPT_VARIANT

SO:0001576 A sequence variant that changes the structure of the transcript (is a: GENE_VARIANT). TRANSCRIPT_VARIANT, /** SO: (is a: GENE_VARIANT)). Not used in Jannovar annotations.

INTERGENIC_REGION

public static final VariantEffect 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). Not used in Jannovar annotations.

CHROMOSOME

public static final VariantEffect 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). Not used in Jannovar annotations.

SEQUENCE_VARIANT

public static final VariantEffect SEQUENCE_VARIANT

SO:0001060 Top level term for variants, can be used for marking "uknown effect". Not used in Jannovar annotations.

Field Detail

IS_SPLICING

public static final com.google.common.base.Predicate<VariantEffect> IS_SPLICING

Predicate for testing whether a VariantEffect is related to splicing.

IS_INTRONIC

public static final com.google.common.base.Predicate<VariantEffect> IS_INTRONIC

Predicate for testing whether a VariantEffect is intronic.

TO_SO_TERM

public static final com.google.common.base.Function<VariantEffect,String> TO_SO_TERM

Function for converting from VariantEffect to SO term String.

TO_LEGACY_NAME

public static final com.google.common.base.Function<VariantEffect,String> TO_LEGACY_NAME

Function for converting from VariantEffect to legacy term.

Method Detail

values

public static VariantEffect[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (VariantEffect c : VariantEffect.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static VariantEffect valueOf(String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

IllegalArgumentException - if this enum type has no constant with the specified name

NullPointerException - if the argument is null

getLegacyTerm

public String getLegacyTerm()

Returns:

Legacy (old Jannovar) id.

getImpact

public PutativeImpact getImpact()

Returns:

PutativeImpact of this effect annotation.

getSequenceOntologyTerm

public String getSequenceOntologyTerm()

Returns:

String with the Sequence Ontology term.

getSequenceOID

public String getSequenceOID()

Returns:

String with the Sequence Ontology ID.

getNumber

public int getNumber()

Forward to ordinal() member function.

Returns:

int with the number used for sorting values of type VariantEffect.

isStructural

public boolean isStructural()

Returns:

true if this VariantEffect annotates structural variants.

isSplicing

public boolean isSplicing()

Returns:

true if this VariantEffect could affect splicing.

isIntronic

public boolean isIntronic()

Returns:

true if equal to CODING_TRANSCRIPT_INTRON_VARIANT or NON_CODING_TRANSCRIPT_INTRON_VARIANT.

isOffExome

public boolean isOffExome()

Returns:

true if the variant effect does not indicate a change affecting the exome, CUSTOM is considered on-exome

See Also:

isOffTranscript()

isOffTranscript

public boolean isOffTranscript()

Returns:

true if the variant effect does not indicate a change affecting a transcript, CUSTOM is considered on-transcript

See Also:

isOffExome()