Evidence profile
SGA QEM trio rare disease screening
Canonical evidence interpretation profile for trio-based whole-genome sequencing in rare Mendelian disease screening.
Technical information
- Profile UID
- sga_qem_trio_rare_disease_v1
- Version
- 1.0
- Visibility
- Community
- Domain
- Clinical Genetics
- Standard
- SGA-QEM-1.0 v1.0
- Maintainer
- Swiss Genomics Association
- Status
- canonical
- Scope
- Trio-based whole-genome sequencing for rare Mendelian disease screening
- Source file
- evidence_interpretation_rules_e7af8e5dc03accac17b690d244995afa.html
- Checksum
- e7af8e5dc03accac17b690d244995afa
How to read this table
Rule name, meaning, and flag describe how available data are interpreted before QuantBayes is run.
Each rule can return TRUE, FALSE, or NA. Under this QEM convention, only FALSE contributes supporting evidence.
Evidence shows the human interpretation. Matrix shows the binary value sent to QuantBayes.
Rules
Evidence interpretation rules
5 rules
| Rule name | Meaning | Flag | Evidence | Matrix |
|---|---|---|---|---|
Parent genotype unavailable parent_gt_unavailable | Parental genetic data are missing, so inheritance cannot be assessed. This contributes 0. | TRUE | No | 0 |
Parent genotype unavailable parent_gt_unavailable | Parental genetic data are available and inheritance can be evaluated. This contributes 1. | FALSE | Yes | 1 |
Parent genotype unavailable parent_gt_unavailable | It is unknown whether parental genetic data are available. This contributes 0. | NA | No | 0 |
Parent genotype mechanistically inconsistent AR parent_gt_mechanistically_inconsistent_ar | Parental results rule out an autosomal recessive explanation. This contributes 0. | TRUE | No | 0 |
Parent genotype mechanistically inconsistent AR parent_gt_mechanistically_inconsistent_ar | Parental results are compatible with autosomal recessive inheritance. This contributes 1. | FALSE | Yes | 1 |
Parent genotype mechanistically inconsistent AR parent_gt_mechanistically_inconsistent_ar | Parental genetic data are missing, so inheritance cannot be checked. This contributes 0. | NA | No | 0 |
Compound heterozygous phase inconsistent compound_het_phase_inconsistent | The two variants are arranged in a way that cannot explain disease together. This contributes 0. | TRUE | No | 0 |
Compound heterozygous phase inconsistent compound_het_phase_inconsistent | The two variants are arranged in a way that could explain disease together. This contributes 1. | FALSE | Yes | 1 |
Compound heterozygous phase inconsistent compound_het_phase_inconsistent | Information on how the variants are arranged is unavailable. This contributes 0. | NA | No | 0 |
De novo mechanism not excluded denovo_mechanism_not_excluded | Family data rule out the variant being a new genetic change. This contributes 0. | TRUE | No | 0 |
De novo mechanism not excluded denovo_mechanism_not_excluded | Family data allow the variant to be a new genetic change. This contributes 1. | FALSE | Yes | 1 |
De novo mechanism not excluded denovo_mechanism_not_excluded | Parental genetic data are missing, so this cannot be assessed. This contributes 0. | NA | No | 0 |
Unaffected relative homozygous ALT unaffected_relative_homozygous_alt | An unaffected family member carries the same genetic change. This contributes 0. | TRUE | No | 0 |
Unaffected relative homozygous ALT unaffected_relative_homozygous_alt | No unaffected family member is known to carry the same change. This contributes 1. | FALSE | Yes | 1 |
Unaffected relative homozygous ALT unaffected_relative_homozygous_alt | Family health or genetic information is insufficient to assess this. This contributes 0. | NA | No | 0 |