Table 1.

Five ClinVar pathogenic immune-related variants annotated as low severity in the reference transcript set but high severity in the custom transcriptome

Variant	Location GRCh38	Allele	Gene	Consequence reference	Consequence custom	ClinVar condition	ClinVar evidence
rs80358236	1:172665641	C	FASLG	In-frame deletion	Start lost & in-frame deletion	Autoimmune lymphoproliferative syndrome	No assertion criteria provided. Citation; PMID: 8787672. No functional evidence.
rs1573262398	2:97724319	T	ZAP70	Benign missense	Missense (unknown)	Combined T and B cell immunodeficiency	Criteria provided, single submitter. No functional evidence, no citation
rs113994173	2:97733464	A	ZAP70	Intron	Missense (unknown)	Combined immunodeficiency due to ZAP70 deficiency	No assertion criteria provided. Citation; PMID: 20301777. No functional evidence.
rs387906763	2:190999647	G	STAT1	Benign missense	Start lost	Immunodeficiency 31 C	Criteria provided, single submitter. Citation; PMID: 21727188. No functional evidence.
rs1236009877	6:137203727	A	IFNGR1	Intron	Stop gained	Immunodeficiency 27 A	Criteria provided, single submitter. No functional evidence, no citation.