From d31a0bd6f61d5025008e89a055188e70269e4e5f Mon Sep 17 00:00:00 2001 From: Sigve Nakken Date: Sat, 8 Jun 2024 00:11:43 +0200 Subject: [PATCH] Remove LOFTEE --- R/classification.R | 24 ++++++++++++------------ vignettes/output.Rmd | 2 +- vignettes/variant_classification.Rmd | 10 +++++----- 3 files changed, 18 insertions(+), 18 deletions(-) diff --git a/R/classification.R b/R/classification.R index a70e47a..dda171a 100644 --- a/R/classification.R +++ b/R/classification.R @@ -253,23 +253,23 @@ assign_pathogenicity_evidence <- function(var_calls, settings, ref_data) { ## Alternate allele absent in the population-specific ## non-cancer gnomAD subset "ACMG_PVS1_1", - ## Null variant - predicted as LoF by LOFTEE - within pathogenic range + ## Null variant - predicted as LoF - within pathogenic range ## - LoF established for gene "ACMG_PVS1_2", - ## Null variant - not predicted as LoF by LOFTEE - + ## Null variant - not predicted as LoF - ## within pathogenic range - LoF established for gene "ACMG_PVS1_3", - ## Null variant - predicted as LoF by LOFTEE - within pathogenic range - + ## Null variant - predicted as LoF - within pathogenic range - ## LoF not established for gene "ACMG_PVS1_4", - ## Null variant - not predicted as LoF by LOFTEE -- + ## Null variant - not predicted as LoF -- ## within pathogenic range - LoF not established for gene "ACMG_PVS1_5", ## start lost - within pathogenic range - Lof established for gene "ACMG_PVS1_6", ## start lost - within pathogenic range - LoF not established for gene "ACMG_PVS1_7", - ## donor/acceptor variant - predicted as LoF by LOFTEE - + ## donor/acceptor variant - predicted as LoF - ## within pathogenic range ## - not last intron - LoF established for gene "ACMG_PVS1_8", @@ -553,21 +553,21 @@ assign_pathogenicity_evidence <- function(var_calls, settings, ref_data) { # presumed loss of mRNA/protein (LOFTEE) or not) # # 'ACMG_PVS1_1' - Null variant (frameshift, nonsense) - - # predicted as LoF by LOFTEE - within pathogenic range - LoF established + # predicted as LoF - within pathogenic range - LoF established # 'ACMG_PVS1_2' - Null variant (frameshift, nonsense) - - # not predicted as LoF by LOFTEE - within pathogenic range - LoF established + # not predicted as LoF - within pathogenic range - LoF established # 'ACMG_PVS1_3' - Null variant (frameshift, nonsense) - - # predicted as LoF by LOFTEE - within pathogenic range - LoF not established + # predicted as LoF - within pathogenic range - LoF not established # 'ACMG_PVS1_4' - Null variant (frameshift, nonsense) - - # not predicted as LoF by LOFTEE -- within pathogenic range - LoF not + # not predicted as LoF -- within pathogenic range - LoF not # established for gene # 'ACMG_PVS1_5' - start lost - within pathogenic range - Lof established # 'ACMG_PVS1_6' - start lost - within pathogenic range - LoF not established - # 'ACMG_PVS1_7' - splice acceptor/donor variant - predicted as LoF by LOFTEE + # 'ACMG_PVS1_7' - splice acceptor/donor variant - predicted as LoF # - not last intron - within pathogenic range - Lof established - # 'ACMG_PVS1_8' - splice acceptor/donor variant - predicted as LoF by LOFTEE + # 'ACMG_PVS1_8' - splice acceptor/donor variant - predicted as LoF # - last intron - within pathogenic range - Lof established - # 'ACMG_PVS1_9' - splice acceptor/donor variant - predicted as LoF by LOFTEE + # 'ACMG_PVS1_9' - splice acceptor/donor variant - predicted as LoF # - not last intron - within pathogenic range - Lof established # 'ACMG_PVS1_10' - splice variant involving a donor at +3A/G, +4A or +5G - # predicted as damaging by insilico predictions - within pathogenic range diff --git a/vignettes/output.Rmd b/vignettes/output.Rmd index c8190c6..8d4f83c 100644 --- a/vignettes/output.Rmd +++ b/vignettes/output.Rmd @@ -348,7 +348,7 @@ The following variables are included in the tiered TSV file (VCF tags in the que | 33. `MUTATION_HOTSPOT` | Cancer mutation hotspot (cancerhotspots.org) | | 34. `RMSK_HIT` | RepeatMasker hit | | 35. `EFFECT_PREDICTIONS` | Functional effect predictions from multiple algorithms (dbNSFP) | -| 36. `LOSS_OF_FUNCTION` | Loss-of-function variant, as predicted from VEP's LofTee plugin | +| 36. `LOSS_OF_FUNCTION` | Loss-of-function variant | | 37. `NULL_VARIANT` | Frameshift or stop-gain variant | | 38. `DBMTS` | variant with potential effect on microRNA target sites (dbMTS). Format: `|||`. _Target prediction algorithms_ indicate support by different algorithms (separated by '&'), `TS` = TargetScan, `M` = miRanda, `R` = RNAhybrid. *Gain_loss_consensus* indicate whether the variant was predicted to disrupt a binding site (`L` = Loss), or create a new target site (`G` = gain) by the different algorithms | | 39. `REGULATORY_ANNOTATION` | Overlap of variant with regulatory elements (VEP) | diff --git a/vignettes/variant_classification.Rmd b/vignettes/variant_classification.Rmd index 5c14f2d..2a7ae82 100644 --- a/vignettes/variant_classification.Rmd +++ b/vignettes/variant_classification.Rmd @@ -31,13 +31,13 @@ The refined ACMG/AMP criteria listed below form the basis for the tier assigned | 12. `ACMG_BP1` (**-0.5**) | Missense variant in a gene for which primarily truncating variants (>90% of pathogenic variants) are known to cause disease (ClinVar) | | 13. `ACMG_PM2_1` (**0.5**) | Allele count within pathogenic range (MAF <= 0.005% in the population-specific non-cancer gnomAD subset) | | 14. `ACMG_PM2_2` (**1**) | Alternate allele absent in the population-specific non-cancer gnomAD subset | -| 15. `ACMG_PVS1_1` (**5**) | Null variant (frameshift/nonsense) - predicted as LoF by LOFTEE - within pathogenic range - LoF established for gene | -| 16. `ACMG_PVS1_2` (**2.5**) | Null variant (frameshift/nonsense) - not predicted as LoF by LOFTEE - within pathogenic range - LoF established for gene | -| 17. `ACMG_PVS1_3` (**2**) | Null variant (frameshift/nonsense) - predicted as LoF by LOFTEE - within pathogenic range - LoF not established for gene | -| 18. `ACMG_PVS1_4` (**0**) | Null variant (frameshift/nonsense) - not predicted as LoF by LOFTEE -- within pathogenic range - LoF not established for gene | +| 15. `ACMG_PVS1_1` (**5**) | Null variant (frameshift/nonsense) - predicted as LoF - within pathogenic range - LoF established for gene | +| 16. `ACMG_PVS1_2` (**2.5**) | Null variant (frameshift/nonsense) - not predicted as LoF - within pathogenic range - LoF established for gene | +| 17. `ACMG_PVS1_3` (**2**) | Null variant (frameshift/nonsense) - predicted as LoF - within pathogenic range - LoF not established for gene | +| 18. `ACMG_PVS1_4` (**0**) | Null variant (frameshift/nonsense) - not predicted as LoF -- within pathogenic range - LoF not established for gene | | 19. `ACMG_PVS1_5` (**2.5**) | Start (initiator methionine) lost - within pathogenic range - Lof established for gene | | 20. `ACMG_PVS1_6` (**2**) | Start (initiator methionine) lost - within pathogenic range - LoF not established for gene | -| 21. `ACMG_PVS1_7` (**4**) | Donor/acceptor variant - predicted as LoF by LOFTEE - within pathogenic range - not last intron - LoF established for gene | +| 21. `ACMG_PVS1_7` (**4**) | Donor/acceptor variant - predicted as LoF - within pathogenic range - not last intron - LoF established for gene | | 22. `ACMG_PVS1_8` (**2.5**) | Donor/acceptor variant - last intron - within pathogenic range - LoF established for gene | | 23. `ACMG_PVS1_9` (**2**) | Donor/acceptor variant - not last intron - within pathogenic range - LoF not established for gene | | 24. `ACMG_PVS1_10` (**2**) | Donor variant at located at the +3, +4 or +5 position of the intron - within the pathogenic range |