From 76cabf8d551706d0c52e7b66e9b65de5f5fa8f3f Mon Sep 17 00:00:00 2001 From: Mike Wilson Date: Fri, 24 May 2024 09:36:17 -0400 Subject: [PATCH 1/2] Update vep csq impact to match VEP --- gnomad/utils/vep.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnomad/utils/vep.py b/gnomad/utils/vep.py index aaa2d7926..c4dbad15d 100644 --- a/gnomad/utils/vep.py +++ b/gnomad/utils/vep.py @@ -30,20 +30,20 @@ "stop_gained", "frameshift_variant", "stop_lost", + "start_lost", # Considered high impact in v105, previously medium ] CSQ_CODING_MEDIUM_IMPACT = [ - "start_lost", # new in v81 "initiator_codon_variant", # deprecated "transcript_amplification", "inframe_insertion", "inframe_deletion", "missense_variant", "protein_altering_variant", # new in v79 - "splice_region_variant", ] CSQ_CODING_LOW_IMPACT = [ + "splice_region_variant", # Considered low impact in v105, previously medium "incomplete_terminal_codon_variant", "start_retained_variant", # new in v92 "stop_retained_variant", From 387ae66c9c9a781cf2ccbd572a38c4307873116b Mon Sep 17 00:00:00 2001 From: Mike Wilson Date: Fri, 24 May 2024 09:49:07 -0400 Subject: [PATCH 2/2] Add link to vep csq impact page --- gnomad/utils/vep.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnomad/utils/vep.py b/gnomad/utils/vep.py index c4dbad15d..f71c921c4 100644 --- a/gnomad/utils/vep.py +++ b/gnomad/utils/vep.py @@ -21,8 +21,9 @@ Versions of VEP used in gnomAD data, the latest version is 105. """ -# Note that this is the current as of v81 with some included for backwards +# Note that this is the current as of v105 with some included for backwards # compatibility (VEP <= 75) +# See: https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html CSQ_CODING_HIGH_IMPACT = [ "transcript_ablation", "splice_acceptor_variant",