RNA splicing evidence enables robust classification of BRCA1 exon 18 variants: Results from the ENIGMA consortium.

Spliceogenic variants in BRCA1 exon 18: the in-frame exon-skipping transcript (Δ18) encodes a non-functional protein lacking homology-directed repair activity.

The ENIGMA consortium characterised the splicing profile of 166 BRCA1 exon 18 variants using minigene assays, with 32 additionally analysed in blood-derived RNA from 51 individuals and 18 in mouse embryonic stem cell assays to assess homology-directed repair capacity. Blood RNA and minigene measurements correlated significantly, and results in murine cells were highly concordant. The in-frame exon 18 skipping transcript (Δ18) encodes a non-functional protein with no rescue activity. Linear regression placed the thresholds compatible with benign repair activity at 59% or more full-length transcript and less than 34% Δ18, values that differ from the ACMG/AMP thresholds recommended by the ClinGen ENIGMA expert panel (more than 30% functional transcripts or less than 70% non-functional transcripts). Incorporating splicing evidence altered the interpretation of 34% of variants and resolved uncertainty in roughly 10% of cases.

Synthesis written by Geno'X. For the full original abstract, please refer to the source publication.

The point that matters is not the catalogue of 166 variants but the finding that usable quantitative thresholds depend on the exon: exon 18 tolerates skipping less well than the generic BP7_strong(RNA) rule assumes, so a globally calibrated ACMG criterion can misclassify locally. The exercise will have to be repeated exon by exon across BRCA1 and BRCA2 before a single threshold can be expected. For a diagnostic laboratory the gain is immediate: roughly 10% of uncertainty resolved in this region, with minigene / blood RNA concordance strong enough to support interpretation.

Analysis by Dr Thibaut Benquey