Classification rationale
PM2
BP4
VUS
LZTR1 c.2417T>G
The LZTR1 c.2417T>G (p.Leu806Trp) variant has not been observed in somatic cancers in COSMIC and has been reported in ClinVar as likely pathogenic by a single clinical laboratory.1 This variant is absent from gnomAD v2.1 and gnomAD v4.1, corresponding to an observed allele frequency of 0 in both datasets.2 Computational evidence supports a benign interpretation because REVEL is 0.174, below the LZTR1 BP4 threshold of 0.3, SpliceAI predicts no splice effect with a maximum delta score of 0.00, and BayesDel is -0.202983.3
PM2 + BP4
→
VUS