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Update VEP csqs in impact categories to match VEP #703

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merged 2 commits into from
May 24, 2024
Merged

Update VEP csqs in impact categories to match VEP #703

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76cabf8
Update vep csq impact to match VEP
mike-w-wilson May 24, 2024
387ae66
Add link to vep csq impact page
mike-w-wilson May 24, 2024
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7 changes: 4 additions & 3 deletions gnomad/utils/vep.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,29 +21,30 @@
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",
"splice_donor_variant",
"stop_gained",
"frameshift_variant",
"stop_lost",
"start_lost", # Considered high impact in v105, previously medium
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it won't let me comment above, but lines 24-25 say:

# Note that this is the current as of v81 with some included for backwards
# compatibility (VEP <= 75)

how about

# 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_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",
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