package seqvars.pbs.query

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Store query information for one case.

Used in: output.OutputHeader

• optional QuerySettingsGenotype genotype = 1

  Genotype query settings.

• optional QuerySettingsQuality quality = 2

  Quality query settings.

• optional QuerySettingsFrequency frequency = 3

  Frequency query settings.

• optional QuerySettingsConsequence consequence = 4

  Consequence query settings.

• optional QuerySettingsLocus locus = 5

  Locus query settings.

• optional QuerySettingsClinVar clinvar = 6

  ClinVar query settings.

Enumeration of canonical ClinVar germline aggregte descriptions.

Used in: QuerySettingsClinVar

• CLINVAR_GERMLINE_AGGREGATE_DESCRIPTION_UNSPECIFIED = 0

  Unknown description.

• CLINVAR_GERMLINE_AGGREGATE_DESCRIPTION_PATHOGENIC = 1

  Pathogenic.

• CLINVAR_GERMLINE_AGGREGATE_DESCRIPTION_LIKELY_PATHOGENIC = 2

  Likely pathogenic.

• CLINVAR_GERMLINE_AGGREGATE_DESCRIPTION_UNCERTAIN_SIGNIFICANCE = 3

  Uncertain significance.

• CLINVAR_GERMLINE_AGGREGATE_DESCRIPTION_LIKELY_BENIGN = 4

  Likely benign.

• CLINVAR_GERMLINE_AGGREGATE_DESCRIPTION_BENIGN = 5

  Benign.

The Variant consequence

Used in: output.ConsequenceCount, output.GeneRelatedConsequences, QuerySettingsConsequence

• CONSEQUENCE_UNSPECIFIED = 0

  Unknown consequence.

  high impact

• CONSEQUENCE_TRANSCRIPT_ABLATION = 1

  Transcript ablation.

• CONSEQUENCE_EXON_LOSS_VARIANT = 2

  Exon loss variant.

• CONSEQUENCE_SPLICE_ACCEPTOR_VARIANT = 3

  Splice acceptor variant

• CONSEQUENCE_SPLICE_DONOR_VARIANT = 4

  Splice donor variant

• CONSEQUENCE_STOP_GAINED = 5

  Stop gained

• CONSEQUENCE_FRAMESHIFT_VARIANT = 6

  Frameshift variant

• CONSEQUENCE_FRAMESHIFT_ELONGATION = 43

  Frameshift elongation

• CONSEQUENCE_FRAMESHIFT_TRUNCATION = 44

  Frameshift truncation

• CONSEQUENCE_STOP_LOST = 7

  Stop lost

• CONSEQUENCE_START_LOST = 8

  Start lost

• CONSEQUENCE_TRANSCRIPT_AMPLIFICATION = 9

  Transcript amplification

• CONSEQUENCE_FEATURE_ELONGATION = 10

  Feature elongation.

• CONSEQUENCE_FEATURE_TRUNCATION = 11

  Feature truncation.

  moderate impact

• CONSEQUENCE_DISRUPTIVE_INFRAME_INSERTION = 12

  Disruptive inframe insertion

• CONSEQUENCE_DISRUPTIVE_INFRAME_DELETION = 13

  Disruptive inframe deletion

• CONSEQUENCE_CONSERVATIVE_INFRAME_INSERTION = 14

  Conservative inframe insertion

• CONSEQUENCE_CONSERVATIVE_INFRAME_DELETION = 15

  Conservative inframe deletion

• CONSEQUENCE_MISSENSE_VARIANT = 16

  Missense variant

• CONSEQUENCE_RARE_AMINO_ACID_VARIANT = 45

  Rare amino acid variant

• CONSEQUENCE_PROTEIN_ALTERING_VARIANT = 46

  Protein altering variant

• CONSEQUENCE_INFRAME_DELETION = 49

  Inframe deletion

• CONSEQUENCE_INFRAME_INSERTION = 50

  Inframe insertion

• CONSEQUENCE_SELENOCYSTEINE_GAIN = 51

  Selenocysteine gain

• CONSEQUENCE_SELENOCYSTEINE_LOSS = 52

  Selenocysteine loss

  low impact

• CONSEQUENCE_SPLICE_DONOR_FIFTH_BASE_VARIANT = 17

  Splice donor 5th base variant.

• CONSEQUENCE_SPLICE_REGION_VARIANT = 18

  Splice region variant.

• CONSEQUENCE_EXONIC_SPLICE_REGION_VARIANT = 47

  Exonic splice region variant.

• CONSEQUENCE_SPLICE_DONOR_REGION_VARIANT = 19

  Splice donor region variant.

• CONSEQUENCE_SPLICE_POLYPYRIMIDINE_TRACT_VARIANT = 20

  Splice polypyrimidine tract variant.

• CONSEQUENCE_START_RETAINED_VARIANT = 21

  Start retained variant.

• CONSEQUENCE_STOP_RETAINED_VARIANT = 22

  Stop retained variant.

• CONSEQUENCE_SYNONYMOUS_VARIANT = 23

  Synonymous variant.

• CONSEQUENCE_INCOMPLETE_TERMINAL_CODON_VARIANT = 53

  Incomplete terminal codon variant

  modifier

• CONSEQUENCE_CODING_SEQUENCE_VARIANT = 24

  Coding sequence variant.

• CONSEQUENCE_MATURE_MIRNA_VARIANT = 25

  Mature miRNA variant.

• CONSEQUENCE_FIVE_PRIME_UTR_EXON_VARIANT = 26

  5' UTR exon variant.

• CONSEQUENCE_FIVE_PRIME_UTR_INTRON_VARIANT = 27

  5' UTR intron variant.

• CONSEQUENCE_FIVE_PRIME_UTR_VARIANT = 54

  5' UTR variant.

• CONSEQUENCE_THREE_PRIME_UTR_EXON_VARIANT = 28

  3' UTR exon variant.

• CONSEQUENCE_THREE_PRIME_UTR_INTRON_VARIANT = 29

  3' UTR intron variant.

• CONSEQUENCE_THREE_PRIME_UTR_VARIANT = 55

  3' UTR variant.

• CONSEQUENCE_NON_CODING_TRANSCRIPT_EXON_VARIANT = 30

  Non-coding transcript exon variant.

• CONSEQUENCE_NON_CODING_TRANSCRIPT_INTRON_VARIANT = 31

  Non-coding transcript intron variant.

• CONSEQUENCE_NON_CODING_TRANSCRIPT_VARIANT = 56

  Non-coding transcript variant.

• CONSEQUENCE_CODING_TRANSCRIPT_INTRON_VARIANT = 48

  Coding transcript intron variant.

• CONSEQUENCE_UPSTREAM_GENE_VARIANT = 32

  Upstream gene variant.

• CONSEQUENCE_DOWNSTREAM_GENE_VARIANT = 33

  Downstream gene variant.

• CONSEQUENCE_TFBS_ABLATION = 34

  TFBS ablation.

• CONSEQUENCE_TFBS_AMPLIFICATION = 35

  TFBS amplification.

• CONSEQUENCE_TF_BINDING_SITE_VARIANT = 36

  TFBS binding site variant.

• CONSEQUENCE_REGULATORY_REGION_ABLATION = 37

  Regulatory region ablation.

• CONSEQUENCE_REGULATORY_REGION_AMPLIFICATION = 38

  Regulatory region amplification.

• CONSEQUENCE_REGULATORY_REGION_VARIANT = 39

  Regulatory region variant.

• CONSEQUENCE_INTERGENIC_VARIANT = 40

  Intergenic variant.

• CONSEQUENCE_INTRON_VARIANT = 41

  Intron variant.

• CONSEQUENCE_GENE_VARIANT = 42

  Gene variant.

Genomic region.

Used in: QuerySettingsLocus

• string chrom = 1

  Chromosome

• optional Range range = 2

  Range of region

Choice for genotype.

Used in: SampleGenotypeChoice

• GENOTYPE_CHOICE_UNSPECIFIED = 0

  Unknown genotype.

• GENOTYPE_CHOICE_ANY = 1

  Any genoype.

• GENOTYPE_CHOICE_REF = 2

  Reference genotype.

• GENOTYPE_CHOICE_HET = 3

  Heterozygous genotype.

• GENOTYPE_CHOICE_HOM = 4

  Homozygous genotype.

• GENOTYPE_CHOICE_NON_HET = 5

  Non-heterozygous genotype.

• GENOTYPE_CHOICE_NON_HOM = 6

  Non-homozygous genotype.

• GENOTYPE_CHOICE_VARIANT = 7

  Variant genotype.

• GENOTYPE_CHOICE_RECESSIVE_INDEX = 8

  Recessive index.

• GENOTYPE_CHOICE_RECESSIVE_FATHER = 9

  Recessive father.

• GENOTYPE_CHOICE_RECESSIVE_MOTHER = 10

  Recessive mother.

In-house filter options.

Used in: QuerySettingsFrequency

• bool enabled = 1

  Whether to enable filtration.

• optional int32 max_het = 2

  Maximal number of heterozygous carriers

• optional int32 max_hom = 3

  Maximal number of homozygous carriers

• optional int32 max_hemi = 4

  Maximal number of hemizygous carriers

• optional int32 max_carriers = 5

  Maximal number of total carriers.

Mitochondrial filter options.

Used in: QuerySettingsFrequency

• bool enabled = 1

  Whether to enable filtration.

• optional int32 max_het = 2

  Maximal number of heteroplasmic carriers.

• optional int32 max_hom = 3

  Maximal number of homoplasmic carriers.

• optional float max_af = 4

  Maximal allele frequency.

gnomAD filter options.

Used in: QuerySettingsFrequency

• bool enabled = 1

  Whether to enable filtration.

• optional int32 max_het = 2

  Maximal number of heterozygous carriers

• optional int32 max_hom = 3

  Maximal number of homozygous carriers

• optional int32 max_hemi = 4

  Maximal number of hemizygous carriers

• optional float max_af = 5

  Maximal allele frequency.

Clinvar-related query settings.

Used in: CaseQuery

• bool presence_required = 1

  Wether to require ClinVar membership

• repeated ClinvarGermlineAggregateDescription germline_descriptions = 2

  The ClinVar germline aggregate description to include.

• bool allow_conflicting_interpretations = 3

  Whether to include conflicting interpretation ClinVar variants

Consequence-related filter settings.

Used in: CaseQuery

• repeated VariantType variant_types = 1

  The variant types.

• repeated TranscriptType transcript_types = 2

  The transcript types.

• repeated Consequence consequences = 3

  List of consequences to consider

• optional int32 max_dist_to_exon = 4

  Maximal distance to next exon, if any

Population frequency filter options.

Used in: CaseQuery

• optional NuclearFrequencySettings gnomad_exomes = 1

  gnomAD-exomes filter

• optional NuclearFrequencySettings gnomad_genomes = 2

  gnomAD-genomes filter

• optional MitochondrialFrequencySettings gnomad_mtdna = 3

  gnomAD-MT filter

• optional MitochondrialFrequencySettings helixmtdb = 4

  HelixMtDb filter

• optional InhouseFrequencySettings inhouse = 5

  In-house filter

Genotype-related filter settings.

Used in: CaseQuery

• RecessiveMode recessive_mode = 1

  Recessive mode

• repeated SampleGenotypeChoice sample_genotypes = 2

  List of sample genotype choices

Locus-related filter settings.

Used in: CaseQuery

• repeated string genes = 1

  List of HGNC identifiers for filtration to genes. The server will expand gene panels to gene lists here.

• repeated GenomicRegion genome_regions = 2

  List of genomic regions to limit restrict the resulting variants to

Per-sample quality filter settings.

Used in: CaseQuery

• repeated SampleQualitySettings sample_qualities = 1

  List of sample quality settings

An 1-based integer range.

Used in: GenomicRegion

• int32 start = 1

  1-based start position.

• int32 stop = 2

  1-based end position.

Enumeration for recessive mode queries.

Used in: QuerySettingsGenotype

• RECESSIVE_MODE_UNSPECIFIED = 0

  Unknown recessive mode.

• RECESSIVE_MODE_DISABLED = 1

  Disabled recessive mode.

• RECESSIVE_MODE_COMPOUND_HETEROZYGOUS = 2

  Compound heterozygous recessive mode.

• RECESSIVE_MODE_HOMOZYGOUS = 3

  Homozygous recessive mode.

• RECESSIVE_MODE_ANY = 4

  Generic recessive mode.

Genotype choice for one sample.

Used in: QuerySettingsGenotype

• string sample = 1

  Name of the sample filtered for

• GenotypeChoice genotype = 2

  Genotype choice

• bool include_no_call = 3

  Whether to include no-call (will disable quality filter).

• bool enabled = 4

  Whether to enable sample in filtration

Quality settings for one sample.

Used in: QuerySettingsQuality

• string sample = 1

  Name of the sample filtered for

• bool filter_active = 2

  Drop whole variant on failure

• optional int32 min_dp_het = 3

  Minimal coverage for het. sites

• optional int32 min_dp_hom = 4

  Minimal coverage for hom. sites

• optional int32 min_gq = 5

  Minimal genotype quality

• optional float min_ab = 6

  Minimal allele balance for het. variants

• optional int32 min_ad = 7

  Minimal number of alternate reads

• optional int32 max_ad = 8

  Maximal number of alternate reads

Transcript types to consider.

Used in: QuerySettingsConsequence

• TRANSCRIPT_TYPE_UNSPECIFIED = 0

  Unknown transcript type.

• TRANSCRIPT_TYPE_CODING = 1

  Coding transcript.

• TRANSCRIPT_TYPE_NON_CODING = 2

  Non-coding transcript.

The variant types.

Used in: QuerySettingsConsequence

• VARIANT_TYPE_UNSPECIFIED = 0

  Unknown variant type

• VARIANT_TYPE_SNV = 1

  SNV

• VARIANT_TYPE_INDEL = 2

  Indel

• VARIANT_TYPE_MNV = 3

  MNV

• VARIANT_TYPE_COMPLEX_SUBSTITUTION = 4

  Complex Substitution