feat: restrict upgrade/downgrade of AMCG seqvar criteria (#291) #321
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #321 +/- ##
==========================================
+ Coverage 75.63% 75.66% +0.03%
==========================================
Files 170 170
Lines 6627 6636 +9
Branches 1464 1463 -1
==========================================
+ Hits 5012 5021 +9
Misses 1428 1428
Partials 187 187
|
holtgrewe
deleted the
291-restrict-the-upgradingdowngrading-of-acmg-seqvar-criteria
branch
xiamaz
requested changes
Dec 21, 2023
| AcmgEvidenceLevel.PathogenicVeryStrong, | ||
| AcmgEvidenceLevel.PathogenicStrong, | ||
| AcmgEvidenceLevel.PathogenicModerate, | ||
| AcmgEvidenceLevel.PathogenicSupporting | ||
| ] | ||
|
|
||
| /** Array of benign evidence levels. */ | ||
| const ACMG_EVIDENCE_LEVELS_BENIGN = [ | ||
| export const ACMG_EVIDENCE_LEVELS_BENIGN = [ | ||
| AcmgEvidenceLevel.BenignStandalone, | ||
| AcmgEvidenceLevel.BenignStrong, |
There was a problem hiding this comment.
Fixed in resolution of #324.
| const ACMG_EVIDENCE_LEVELS_PATHOGENIC_VS_S_M = [ | ||
| AcmgEvidenceLevel.PathogenicVeryStrong, | ||
| AcmgEvidenceLevel.PathogenicStrong, | ||
| AcmgEvidenceLevel.PathogenicModerate |
There was a problem hiding this comment.
Why are you defining these in separate arrays?
There was a problem hiding this comment.
This makes it a bit easier to read where they are used in my opinion.
| (e.g., active site of an enzyme) without benign variation.` | ||
| description: `Located in a mutational hot spot and/or critical and well-established functional domain | ||
| (e.g., active site of an enzyme) without benign variation.`, | ||
| evidenceLevels: ACMG_EVIDENCE_LEVELS_PATHOGENIC_S_M_P | ||
| }, | ||
| { | ||
| criteria: AcmgCriteria.PM2, | ||
| defaultEvidenceLevel: AcmgEvidenceLevel.PathogenicModerate, |
There was a problem hiding this comment.
Below only supporting allowed. As long as you only use defaultEvidenceLevel for grouping and sorting, this should be fine.
| }, | ||
| { | ||
| criteria: AcmgCriteria.BP7, | ||
| defaultEvidenceLevel: AcmgEvidenceLevel.BenignSupporting, | ||
| label: 'BP7', | ||
| hint: 'silent, no splicing/conservation', | ||
| description: | ||
| 'A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved' | ||
| 'A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved', | ||
| evidenceLevels: ACMG_EVIDENCE_LEVELS_BENIGN_P |
There was a problem hiding this comment.
In newer papers can be more flexibly set to BS, BM or BP
There was a problem hiding this comment.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.