Table 2.

GnomAD variants in clinical genes for which the BIOS-trained model predicts ASE effects.

Gene	RsID/GRCh37	MAF	Conseq.	ClinVar
BRCA2	rs748508287	3.99E−06	Stop gained	P***
BRCA2	rs80358556	4.01E−06	Stop gained	P***
BRCA2	rs80358851	3.99E−06	Stop gained	P***
BRCA2	rs766337502	4.60E−06	Intronic	–
BRCA2	rs753979600	4.56E−06	Intronic	–
BRCA2	rs779588681	4.69E−06	Intronic	–
BRCA2	rs80359003	7.95E−06	Stop gained	P***
BRCA2	rs776353983 (C>A)	3.98E−06	Stop gained	P***
NF1	rs764079291	4.00E−06	Stop gained	P**
NF1	rs1316926587	4.00E−06	Stop gained	P*
NF1	rs761199437	0	Stop gained	–
NF1	rs1282299543	0	Stop gained	P*
NF1	rs376576925 (C>A)	1.59E−05	Synonymous	LB/VUS*
NF1	rs376576925 (C>T)	3.98E−06	Stop gained	P**
NF1	17:29576138G>A	3.98E−06	Splice donor	P**
NF1	rs748461474	8.04E−06	Intronic	–
NF1	rs776167625	4.02E−06	Intronic	–
NF1	rs1481561333	4.02E−06	Intronic	–
NF1	rs756300767	8.32E−06	Intronic	–
RET	rs754967305	3.12E−05	Intronic	LB**
RET	10:43596200T>C	0	Intronic	–
RET	rs1452567543	4.38E−05	Intronic	–
RET	rs1198523793	0	Intronic	–
RET	rs979417275	3.67E−05	Intronic	–
RET	rs1471253713	0	Intronic	–
RET	rs1476675800	0	Stop gained	–
RET	rs775711017	0	Stop gained	–

The ClinVar classifications shown are: P for Pathogenic, LB for Likely Benign, and VUS for Variant of Unknown Significance. The asterisks indicate the review status of ClinVar, where zero is the worst and four is the best. The MAF (Minor Allele Frequency) values are taken from GnomAD exomes r2.1.1. A MAF of zero means the variant was detected but there were no high-confidence genotype calls made. The RS identifiers are supplemented with base changes in ambiguous cases. GRCh37 coordinates are used if no RS identifiers exist for an SNV.