org.opencb.biodata.models.variant.avro.EvidenceImpact Maven / Gradle / Ivy
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/**
* Autogenerated by Avro
*
* DO NOT EDIT DIRECTLY
*/
package org.opencb.biodata.models.variant.avro;
@SuppressWarnings("all")
/** Evidence of pathogenicity and benign impact as defined in Richards, S. et al. (2015). Standards and guidelines for the interpretation
of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and
the Association for Molecular Pathology. Genetics in Medicine, 17(5), 405–423. https://doi.org/10.1038/gim.2015.30
Evidence of pathogenicity:
* `very_strong`:
- PVS1 null variant (nonsense, frameshift, canonical ±1 or 2 splice sites, initiation codon, single or multiexon
deletion) in a gene where LOF is a known mechanism of disease
* `strong`:
- PS1 Same amino acid change as a previously established pathogenic variant regardless of nucleotide change
- PS2 De novo (both maternity and paternity confirmed) in a patient with the disease and no family history
- PS3 Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene
product
- PS4 The prevalence of the variant in affected individuals is significantly increased compared with the prevalence
in controls
* `moderate`:
- PM1 Located in a mutational hot spot and/or critical and well-established functional domain (e.g., active site of
an enzyme) without benign variation
- PM2 Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes
Project, or Exome Aggregation Consortium
- PM3 For recessive disorders, detected in trans with a pathogenic variant
- PM4 Protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss
variants
- PM5 Novel missense change at an amino acid residue where a different missense change determined to be pathogenic
has been seen before
- PM6 Assumed de novo, but without confirmation of paternity and maternity
* `supporting`:
- PP1 Cosegregation with disease in multiple affected family members in a gene definitively known to cause the
disease
- PP2 Missense variant in a gene that has a low rate of benign missense variation and in which missense variants are
a common mechanism of disease
- PP3 Multiple lines of computational evidence support a deleterious effect on the gene or gene product
(conservation, evolutionary, splicing impact, etc.)
- PP4 Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology
- PP5 Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory
to perform an independent evaluation
Evidence of benign impact:
* `stand_alone`:
- BA1 Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation
Consortium
* `strong`:
- BS1 Allele frequency is greater than expected for disorder
- BS2 Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked
(hemizygous) disorder, with full penetrance expected at an early age
- BS3 Well-established in vitro or in vivo functional studies show no damaging effect on protein function or
splicing
- BS4 Lack of segregation in affected members of a family
* `supporting`:
- BP1 Missense variant in a gene for which primarily truncating variants are known to cause disease
- BP2 Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis
with a pathogenic variant in any inheritance pattern
- BP3 In-frame deletions/insertions in a repetitive region without a known function
- BP4 Multiple lines of computational evidence suggest no impact on gene or gene product (conservation,
evolutionary, splicing impact, etc.)
- BP5 Variant found in a case with an alternate molecular basis for disease
- BP6 Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to
perform an independent evaluation
- BP7 A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice
consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved */
@org.apache.avro.specific.AvroGenerated
public enum EvidenceImpact {
very_strong, strong, moderate, supporting, stand_alone ;
public static final org.apache.avro.Schema SCHEMA$ = new org.apache.avro.Schema.Parser().parse("{\"type\":\"enum\",\"name\":\"EvidenceImpact\",\"namespace\":\"org.opencb.biodata.models.variant.avro\",\"doc\":\"Evidence of pathogenicity and benign impact as defined in Richards, S. et al. (2015). Standards and guidelines for the interpretation\\n of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and\\n the Association for Molecular Pathology. Genetics in Medicine, 17(5), 405–423. https://doi.org/10.1038/gim.2015.30\\n\\nEvidence of pathogenicity:\\n* `very_strong`:\\n - PVS1 null variant (nonsense, frameshift, canonical ±1 or 2 splice sites, initiation codon, single or multiexon\\n deletion) in a gene where LOF is a known mechanism of disease\\n* `strong`:\\n - PS1 Same amino acid change as a previously established pathogenic variant regardless of nucleotide change\\n - PS2 De novo (both maternity and paternity confirmed) in a patient with the disease and no family history\\n - PS3 Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene\\n product\\n - PS4 The prevalence of the variant in affected individuals is significantly increased compared with the prevalence\\n in controls\\n* `moderate`:\\n - PM1 Located in a mutational hot spot and/or critical and well-established functional domain (e.g., active site of\\n an enzyme) without benign variation\\n - PM2 Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes\\n Project, or Exome Aggregation Consortium\\n - PM3 For recessive disorders, detected in trans with a pathogenic variant\\n - PM4 Protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss\\n variants\\n - PM5 Novel missense change at an amino acid residue where a different missense change determined to be pathogenic\\n has been seen before\\n - PM6 Assumed de novo, but without confirmation of paternity and maternity\\n* `supporting`:\\n - PP1 Cosegregation with disease in multiple affected family members in a gene definitively known to cause the\\n disease\\n - PP2 Missense variant in a gene that has a low rate of benign missense variation and in which missense variants are\\n a common mechanism of disease\\n - PP3 Multiple lines of computational evidence support a deleterious effect on the gene or gene product\\n (conservation, evolutionary, splicing impact, etc.)\\n - PP4 Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology\\n - PP5 Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory\\n to perform an independent evaluation\\n\\nEvidence of benign impact:\\n* `stand_alone`:\\n - BA1 Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation\\n Consortium\\n* `strong`:\\n - BS1 Allele frequency is greater than expected for disorder\\n - BS2 Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked\\n (hemizygous) disorder, with full penetrance expected at an early age\\n - BS3 Well-established in vitro or in vivo functional studies show no damaging effect on protein function or\\n splicing\\n - BS4 Lack of segregation in affected members of a family\\n* `supporting`:\\n - BP1 Missense variant in a gene for which primarily truncating variants are known to cause disease\\n - BP2 Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis\\n with a pathogenic variant in any inheritance pattern\\n - BP3 In-frame deletions/insertions in a repetitive region without a known function\\n - BP4 Multiple lines of computational evidence suggest no impact on gene or gene product (conservation,\\n evolutionary, splicing impact, etc.)\\n - BP5 Variant found in a case with an alternate molecular basis for disease\\n - BP6 Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to\\n perform an independent evaluation\\n - BP7 A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice\\n consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved\",\"symbols\":[\"very_strong\",\"strong\",\"moderate\",\"supporting\",\"stand_alone\"]}");
public static org.apache.avro.Schema getClassSchema() { return SCHEMA$; }
}