owencqueen/cgbench_data huggingface dataset:
Gene: HNF4A (HGNC:5024)
Evidence Code: PVS1 — Strong
Modification Type: Strength
Use 
HNF4A
 PVS1 decision tree.




“Exon skipping or use of a cryptic splice site that preserves reading frame” and “Single to multi-exon deletion that preserves reading frame” 


Exons 5 (LRG 7), 7 (LRG 9), 8 (LRG 10), 9 (LRG 11) - deletion or skipping causes in-frame deletion, 52/52/79/51-79 AA deleted, that is >10 % of the protein in each case - PVS1_Strong  


Exon 10 (LRG 12) - 46 AA, contains the transactivation domain, includes stop loss - PVS1_Strong






Apply PVS1_Strong to initiation codon variants.  MDEP has classified two start codon variants as likely pathogenic (c.3G>A: PM2_Supporting + PP4_Moderate + PP1_Strong + PVS1_Moderate (c.1delA); c.1delA: PM2_Supporting + PP1 + PP4_Moderate + PVS1_Moderate) and there are multiple P/LP variants before the next methionine, p.Met71.