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Remove LOFTEE
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@sigven
sigven committed Jun 7, 2024
1 parent 5ca4659 commit d31a0bd
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Showing 3 changed files with 18 additions and 18 deletions.
24 changes: 12 additions & 12 deletions R/classification.R
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Expand Up @@ -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",
Expand Down Expand Up @@ -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
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2 changes: 1 addition & 1 deletion vignettes/output.Rmd
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Expand Up @@ -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: `<ensembl_transcript_id>|<microrna_identifier>|<target_prediction_algorithms>|<gain_loss_consensus>`. _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) |
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10 changes: 5 additions & 5 deletions vignettes/variant_classification.Rmd
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Expand Up @@ -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 |
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