# ACMG criteria and classification
This documentation is a work in progress and is not currently up to date.
Please contact developers for more details.
# ACMG rules engine
Rules for suggested ACMG criteria are defined in JSON format in:
/src/rule_engine/README for details.
# User group rules
User group-specific ACMG value rules. See
/src/vardb/testdata/usergroups.json for examples.
usergroups.json(see user groups)
The following subkeys define thresholds and values that act as input for the ACMG rules engine, for the given user group:
| ||The population frequency threshold for ACMG criteria BA1 ( ||0-1|
| ||The minimum "allele number" (observed chromosomes at a given locus) for each sub-population.||[integer]|
| ||Whether only missense ( |
| ||Whether the last exon is important ( |
* Similar to filter frequency thresholds, with possibilities for separation of dataset groups and inheritance modes.
# Gene-specific overrides
To define rules for given genes only (within a user group), place the above subkeys within the
config.acmg.genes key, providing a HGNC ID for each gene the rules should apply to.
In addition, the subkey
comment can be defined, specifying information relevant to evaluation of more/all variants in a gene as free text.
# ACMG descriptions
short_criteria) and long (
criteria) descriptions and any
notes for each ACMG criterion and REQ (shown in UI pop-ups) are given in:
For REQs, you can also define which ACMG criteria the REQ relates to in this file, using the key
Sort order and time to outdated (how long an interpretation is considered valid) for clinical classifications is given in:
/example_config.yml for examples.