package seqvars.pbs.output

Get desktop application:
View/edit binary Protocol Buffers messages

Enumeration describing aggregate germline review status value.

Used in: ClinvarAnnotation

• AGGREGATE_GERMLINE_REVIEW_STATUS_UNSPECIFIED = 0

  unspecified aggregate germline review status value

• AGGREGATE_GERMLINE_REVIEW_STATUS_NO_CLASSIFICATION_PROVIDED = 1

  corresponds to "no classification provided"

• AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED = 2

  corresponds to "no assertion criteria provided"

• AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER = 3

  corresponds to "criteria provided, single submitter"

• AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS = 4

  corresponds to "criteria provided, multiple submitters, no conflicts"

• AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_CONFLICTING_CLASSIFICATIONS = 5

  corresponds to "criteria provided, conflicting classifications"

• AGGREGATE_GERMLINE_REVIEW_STATUS_REVIEWED_BY_EXPERT_PANEL = 6

  corresponds to "reviewed by expert panel"

• AGGREGATE_GERMLINE_REVIEW_STATUS_PRACTICE_GUIDELINE = 7

  corresponds to "practice guideline"

• AGGREGATE_GERMLINE_REVIEW_STATUS_NO_CLASSIFICATIONS_FROM_UNFLAGGED_RECORDS = 8

  corresponds to "no classifications from unflagged records"

• AGGREGATE_GERMLINE_REVIEW_STATUS_NO_CLASSIFICATION_FOR_THE_SINGLE_VARIANT = 9

  corresponds to "no classification for the single variant"

Store call-related annotation.

Used in: VariantAnnotation

• repeated SampleCallInfo call_infos = 1

  Store call information for each sample.

ClinGen dosage annotation.

Used in: GeneRelatedConstraints

• ClingenDosageScore haplo = 1

  Haploinsufficiency score.

• ClingenDosageScore triplo = 2

  Triplosensitivity score.

/ Enumeration for Haploinsufficiency / Triplosensitivity scores.

Used in: ClingenDosageAnnotation

• CLINGEN_DOSAGE_SCORE_UNSPECIFIED = 0

  Unspecified

• CLINGEN_DOSAGE_SCORE_SUFFICIENT_EVIDENCE_AVAILABLE = 1

  Sufficient evidence for dosage pathogenicity

• CLINGEN_DOSAGE_SCORE_SOME_EVIDENCE_AVAILABLE = 2

  Some evidence for dosage pathogenicity

• CLINGEN_DOSAGE_SCORE_LITTLE_EVIDENCE = 3

  Little evidence for dosage pathogenicity

• CLINGEN_DOSAGE_SCORE_NO_EVIDENCE_AVAILABLE = 4

  No evidence available

• CLINGEN_DOSAGE_SCORE_RECESSIVE = 5

  Gene associated with autosomal recessive phenotype

• CLINGEN_DOSAGE_SCORE_UNLIKELY = 6

  Dosage sensitivity unlikely

ClinVar-related annotation.

Used in: VariantRelatedAnnotation

• string vcv_accession = 1

  VCV accession.

• string germline_significance_description = 2

  Aggregate germline significance description.

• AggregateGermlineReviewStatus germline_review_status = 3

  Aggregate germline review status.

• string effective_germline_significance_description = 4

  Effective (aka "worst") germline significance description.

Store consequence statistics.

Used in: OutputStatistics

• query.Consequence consequence = 1

  Consequence.

• uint32 count = 2

  Number of records.

Database identifiers.

Used in: VariantRelatedAnnotation

• optional string dbsnp_id = 1

  dbSNP ID.

DECIPHER constraint information.

Used in: GeneRelatedConstraints

• float p_hi = 1

  HI percentile

• float hi_index = 2

  HI raw score

Population frequency information.

Used in: VariantRelatedAnnotation

• optional NuclearFrequency gnomad_exomes = 1

  gnomAD-exomes filter

• optional NuclearFrequency gnomad_genomes = 2

  gnomAD-genomes filter

• optional MitochondrialFrequency gnomad_mtdna = 3

  gnomAD-MT filter

• optional MitochondrialFrequency helixmtdb = 4

  HelixMtDb filter

• optional NuclearFrequency inhouse = 5

  In-house filter

Gene identity related information.

Used in: GeneRelatedAnnotation

• string hgnc_id = 1

  HGNC ID.

• string gene_symbol = 2

  HGNC symbol.

Store gene-related annotation (always for a single gene).

Used in: VariantAnnotation

• optional GeneIdentity identity = 1

  Gene ID information.

• optional GeneRelatedConsequences consequences = 2

  Gene-related consequences, if any (none if intergenic).

• optional GeneRelatedPhenotypes phenotypes = 3

  Gene-related phenotype information, if any.

• optional GeneRelatedConstraints constraints = 4

  Gene-wise constraints on the gene, if any.

/ Gene-related consequences of a variant.

Used in: GeneRelatedAnnotation

• optional string hgvs_t = 1

  HGVS. {c,n} code of variant.

• optional string hgvs_p = 2

  HGVS.p code of variant.

• repeated query.Consequence consequences = 3

  Predicted variant consequences.

• optional string tx_accession = 4

  Transcript accession without version.

• optional int32 tx_version = 5

  Transcript version.

• VariantLocation location = 6

  Whether exon or intron is hit.

• optional int32 rank_ord = 7

  Exon/intron number (1-based).

• optional int32 rank_total = 8

  Exon/intron total count.

Gene-wise constraints.

Used in: GeneRelatedAnnotation

• optional GnomadConstraints gnomad = 1

  gnomAD constraints

• optional DecipherConstraints decipher = 2

  DECIPHER constraints

• optional RcnvConstraints rcnv = 3

  RCNV constraints

• optional ShetConstraints shet = 4

  sHET constraints

• optional ClingenDosageAnnotation clingen = 5

  ClinGen dosage annotation

Phenotype-related information, if any.

Used in: GeneRelatedAnnotation

• bool is_acmg_sf = 1

  ACMG supplementary finding list.

• bool is_disease_gene = 2

  Whether is a known disease gene.

• repeated ModeOfInheritance mode_of_inheritances = 3

  Linked modes of inheritance.

Enumeration of the genome release.

Used in: OutputHeader, VcfVariant

• GENOME_RELEASE_UNSPECIFIED = 0

  Unspecified genome release.

• GENOME_RELEASE_GRCH37 = 1

  GRCh37.

• GENOME_RELEASE_GRCH38 = 2

  GRCh38.

gnomAD constraint information.

Used in: GeneRelatedConstraints

• float mis_z = 1

  mis_z score

• float oe_lof = 2

  oe_lof score

• float oe_lof_lower = 3

  oe_lof_lower score

• float oe_lof_upper = 4

  oe_lof_upper score (LOEF)

• float oe_mis = 5

  oe_mis score

• float oe_mis_lower = 6

  oe_mis_lower score

• float oe_mis_upper = 7

  oe_mis_upper score

• float pli = 8

  pLI score

• float syn_z = 9

  syn_z score

Mitochondrial frequency information.

Used in: FrequencyAnnotation

• int32 an = 1

  Number of covered alleles.

• int32 het = 2

  Number of heteroplasmic carriers.

• int32 homalt = 3

  Number of homoplasmic carriers.

• float af = 4

  Allele frequency.

Enumerations with modes of inheritance from HPO.

Used in: GeneRelatedPhenotypes

• MODE_OF_INHERITANCE_UNSPECIFIED = 0

  Unspecified mode of inheritance.

• MODE_OF_INHERITANCE_AUTOSOMAL_DOMINANT = 1

  Autosomal dominant inheritance (HP:0000006).

• MODE_OF_INHERITANCE_AUTOSOMAL_RECESSIVE = 2

  Autosomal recessive inheritance (HP:0000007).

• MODE_OF_INHERITANCE_X_LINKED_DOMINANT = 3

  X-linked dominant inheritance (HP:0001419).

• MODE_OF_INHERITANCE_X_LINKED_RECESSIVE = 4

  X-linked recessive inheritance (HP:0001423).

• MODE_OF_INHERITANCE_Y_LINKED = 5

  Y-linked inheritance (HP:0001450).

• MODE_OF_INHERITANCE_MITOCHONDRIAL = 6

  Mitochondrial inheritance (HP:0001427).

gnomAD and in-house frequency information.

Used in: FrequencyAnnotation

• int32 an = 1

  Number of covered alleles.

• int32 het = 2

  Number of in-house heterozygous carriers

• int32 homalt = 3

  Number of in-house homozygous carriers

• int32 hemialt = 4

  Number of in-house hemizygous carriers

• float af = 5

  Allele frequency.

Store meta information about query results.

• GenomeRelease genome_release = 1

  Genome release.

• repeated VersionEntry versions = 2

  Versions for each used database or software.

• optional query.CaseQuery query = 3

  The used query settings.

• string case_uuid = 4

  Case UUID.

• optional ResourcesUsed resources = 5

  Resources used.

• optional OutputStatistics statistics = 6

  Statistics about results.

• repeated VariantScoreColumn variant_score_columns = 7

  Information about the variant scores in the output.

Store one record in the output.

• string uuid = 1

  UUID of the record.

• string case_uuid = 2

  Case UUID.

• optional VcfVariant vcf_variant = 3

  The description.

• optional VariantAnnotation variant_annotation = 4

  The variant annotation payload.

Store statistics about the output.

Used in: OutputHeader

• uint64 count_total = 1

  Total number of records.

• uint64 count_passed = 2

  Number of passed records.

• repeated ConsequenceCount passed_by_consequences = 3

  Passed records by consequence.

RCNV constraint information from PMID:35917817

Used in: GeneRelatedConstraints

• float p_haplo = 1

  pHaplo score

• float p_triplo = 2

  pTriplo score

Query resource requirements.

Used in: OutputHeader

• optional google.protobuf.Timestamp start_time = 1

  Start time.

• optional google.protobuf.Timestamp end_time = 2

  End time.

• uint64 memory_used = 3

  RAM usage in bytes.

Store call information for one sample.

Used in: CallRelatedAnnotation

• string sample = 1

  Name of the sample.

• optional string genotype = 2

  Genotype.

• optional int32 dp = 3

  Depth of coverage.

• optional int32 ad = 4

  Alternate read depth.

• optional float gq = 5

  Genotype quality.

• optional int32 ps = 6

  Phase set ID.

Score annotations.

Used in: VariantRelatedAnnotation

• repeated ScoreEntry entries = 1

  Key/value pairs for scores.

Score entry.

Used in: ScoreAnnotations

• string key = 1

  Key.

• optional google.protobuf.Value value = 2

  Value.

sHET constraint information from PMID:31004148

Used in: GeneRelatedConstraints

• float s_het = 1

  sHet score

Transcript type.

• TRANSCRIPT_TYPE_UNSPECIFIED = 0

  Unknown transcript type.

• TRANSCRIPT_TYPE_CODING = 1

  Coding transcript.

• TRANSCRIPT_TYPE_NON_CODING = 2

  Non-coding transcript.

Store the variant annotation payload (always for a single gene).

Used in: OutputRecord

• optional GeneRelatedAnnotation gene = 1

  Gene-related annotation.

• optional VariantRelatedAnnotation variant = 2

  Variant-related annotation.

• optional CallRelatedAnnotation call = 3

  Call-related annotation.

Location where the variant falls in relation to a transcript.

Used in: GeneRelatedConsequences

• VARIANT_LOCATION_UNSPECIFIED = 0

  Unspecified location.

• VARIANT_LOCATION_UPSTREAM = 1

  Upstream of gene.

• VARIANT_LOCATION_EXON = 2

  Exonic.

• VARIANT_LOCATION_INTRON = 3

  Intronic.

• VARIANT_LOCATION_DOWNSTREAM = 4

  Downstream of the gene.

Store variant-related annotation.

Used in: VariantAnnotation

• optional DbIds dbids = 1

  Database identifiers.

• optional FrequencyAnnotation frequency = 2

  Frequency annotation.

• optional ClinvarAnnotation clinvar = 3

  ClinVar annotation.

• optional ScoreAnnotations scores = 4

  Score annotations.

Store information about the variant scores in the output.

Used in: OutputHeader

• string name = 1

  Name of the score.

• string label = 2

  Label for the score.

• string description = 3

  Description of the score.

• VariantScoreColumnType type = 4

  Type of the score.

Enumeration of the variant score type.

Used in: VariantScoreColumn

• VARIANT_SCORE_COLUMN_TYPE_UNSPECIFIED = 0

  Unspecified variant score type.

• VARIANT_SCORE_COLUMN_TYPE_NUMBER = 1

  Number

• VARIANT_SCORE_COLUMN_TYPE_STRING = 2

  String

Store a sequnce variant in VCF representation.

Used in: OutputRecord

• GenomeRelease genome_release = 1

  Genome release.

• string chrom = 2

  Chromosome, normalized.

• int32 chrom_no = 3

  Chromosome number for sorting.

• int32 pos = 4

  1-based position.

• string ref_allele = 5

  Reference allele.

• string alt_allele = 6

  Alternative allele.

Store version information.

Used in: OutputHeader

• string name = 1

  Name of the version.

• string version = 2

  Version string.