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Scores and documentation of ACMG evidence criteria used for variant classification in CPSR

Source: R/data.R
acmg.Rd

Scores and documentation of ACMG evidence criteria used for variant classification in CPSR

Usage

acmg

Format

A list object with three elements: 'score2tier', 'evidence_codes', 'pathogenic_range_gnomad'

score2tier - A data frame with 5 rows and two columns that indicate current score thresholds for variant classification in CPSR:

  • CPSR_CLASSIFICATION - variant classification level (P, LP, VUS etc)

  • CPSR_PATHOGENICITY_SCORE - indication of CPSR "score bucket" for a given classification (HTML string)

#' @format evidence_codes - A data frame with 34 rows and 7 columns that document all ACMG evidence criteria that are used for variant classification in CPSR:

  • cpsr_evidence_code - code for evidence criterion ('ACMG_BA1_AD' etc)

  • category - type of evidence feature ('clinpop','funcvarpop','funcvar','funccomp')

  • pathogenicity_pole - whether the given evidence support a benign variant character ('B'), or pathogenic character ('P')

  • category_long - long version of 'category' column

  • description - Verbose description for the given evidence criterion

  • sherloc_code - Corresponding code identifier in SherLoc (Nykamp et al., GiM, 2017)

  • path_score - Score associated with the given evidence criterion (negative or positive)