-
Can civicbot revise evidence direction and clinical significance for all predisposing evidence to NA?
-
Talked to Lucas and Kerryn about CNV classifications
They use [2020 ACMG CNV guidelines](https://pubmed.ncbi.nlm.nih.gov/31690835/)
Biggest questions are:
* Is gene LOF
* If CNV is not whole gene, t…
-
I tried out AnnotSV v3.0.4 for about 20 samples, and none of their SVs are scored rank-2 in `ACMG_class` column. Here is an ranks for one of the WGS samples:
```sh
$cat out.tsv | awk 'BEGIN{FS="\t…
-
Starting a new ticket specifically dedicated to the question of whether to lump or split representation of Variant Pathogenicity and Variant Oncogenicity Statement types.
This discussion was start…
-
The ClinVar whitelist option (default = true) will set all P/LP 2*+ variants found in a VCF file to have a score of 1.0.
The issue with this is that, while it works well for pathogenic variants, it…
-
**Background**
Currently there are 21+ gene-specific modifications of the ACMG guidelines that should be consulted when curating to determine gene-specific thresholds for each criterion. For example, …
sksmi updated
3 years ago
-
Several predictors have been recommended/requested to be added to the VCI Variant Type predictors table, additionally the predictor table should be updated to be in line with Pejaver et al 2022 and St…
-
Weitere Kommentare / Nachfragen:
* Auf art-decor.org ist die Readtiefe (Read Depth) als String-Value definiert, hier wäre Integer ≥ 0 wünschenswert
* Als Type von Methode ist Code spezifiziert. Welc…
-
Our current recommendation follows the ACMG set f clinical significance terms (P, LP, B, LB, VUS). But this approach conflates the significance classification with the asserting agent's confidence th…
-
I'm trying to figure out why PM1 is scored as 1 for a variant. The variant is:
(hg19) 11:36615436C>T - RAG2 NM_001243786:exon3:c.G283A:p.G95R
I checked the PM1 check function:
```
def check_PM1(…