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. |