BRCA1 c.212+3A>G, p.?

Rule

Apply PS3 when well-established functional studies support a damaging effect; for this variant ENIGMA Table 9 assigns PS3 Strong.

Evidence considered

• ENIGMA Table 9 lists BRCA1 c.212+3A>G as PS3 Strong.
• Supplementary Table 4 classifies c.212+3A>G as Functional impact - complete.
• Supplementary splicing tables summarize 5/6 assays as supporting out-of-frame aberrant transcripts consistent with loss of function.

Sources

Rule

Apply PP3 for intronic variants outside donor/acceptor 1,2 positions when SpliceAI >=0.2.

Evidence considered

• SpliceAI max delta score = 0.63.
• ENIGMA PP3 threshold for predicted splicing impact is SpliceAI >=0.2.

Sources

Rule

PP5 is not applicable in the ENIGMA BRCA1 specification.

Evidence considered

• The BRCA1 ENIGMA specification marks PP5 as not applicable.
• ClinVar classifications are available but do not substitute for independent evidence review under this framework.
• ClinVar expert panel classification

Sources

Rule

PS4 requires a significant excess in affected individuals compared with controls with p-value <=0.05 and OR >=4.

Evidence considered

• ClinVar contains multiple pathogenic submissions and expert-panel review.
• Published reports describe the variant in hereditary breast/ovarian cancer families.
• No qualifying ENIGMA-compatible case-control statistic was identified.

Still missing

• A qualifying case-control analysis would be needed to apply PS4.

Sources

Rule

ENIGMA PM2_Supporting requires absence from controls in the specified gnomAD datasets with adequate coverage.

Evidence considered

• Absent from gnomAD v2.1.
• Present in gnomAD v4.1 at 2/1574274 alleles.
• Observed frequency remains very low but not zero.

Still missing

• If ENIGMA PM2 is reconsidered
• confirm the required dataset version and read-depth criteria for this locus.

Sources

Rule

Apply PP4 only when the combined multifactorial clinical-data LR reaches at least 2.08.

Evidence considered

• Clinical-history LR = 1.061794714953085.
• N_Probands = 1.
• PP4 Supporting requires LR >=2.08.

Sources

Rule

Apply BA1 only when FAF is above 0.1% in a non-founder population.

Evidence considered

• gnomAD v4.1 grpmax FAF = 2.9e-07.
• BA1 requires FAF >0.001.

Sources

Rule

Apply BS1 based on FAF thresholds in non-founder populations.

Evidence considered

• gnomAD v4.1 grpmax FAF = 2.9e-07.
• BS1 Supporting requires FAF >0.00002 and <=0.0001.
• BS1 Strong requires FAF >0.0001.

Sources

Rule

BS3 requires well-established studies showing no damaging effect.

Evidence considered

• ENIGMA Table 9 assigns PS3 Strong
• not BS3.
• Supplementary tables classify the variant as complete functional impact with aberrant splicing.

Sources

Rule

Apply BP4 to intronic variants outside +/-1,2 only when SpliceAI <=0.1.

Evidence considered

• SpliceAI max delta score = 0.63.
• BP4 for this variant type requires SpliceAI <=0.1.

Sources

Rule

Apply BP5 only when the combined multifactorial clinical-data LR is 0.48 or lower.

Evidence considered

• Clinical-history LR = 1.061794714953085.
• N_Probands = 1.
• BP5 Supporting requires LR <=0.48.

Sources

Rule

BP7 requires either RNA evidence showing no damaging effect or, for selected intronic positions, benign computational evidence meeting the BP4 rule.

Evidence considered

• SpliceAI max delta score = 0.63.
• Supplementary RNA studies show aberrant transcripts consistent with loss of function.
• BP7 Supporting bioinformatic rule is for variants at or beyond +7/-21 if BP4 is met.

Sources

Rule

ENIGMA PVS1 applies to null variants, including canonical +/-1,2 splice variants, or to mRNA-only functional evidence when an appropriate PVS1(RNA) strength can be assigned.

Evidence considered

• BRCA1 loss of function is an established disease mechanism in the ENIGMA BRCA1 framework.
• The generic PVS1 scaffold does not treat +3 donor variants as default PVS1 null variants.
• Supplementary ENIGMA splicing tables report aberrant transcripts consistent with loss of function for c.212+3A>G.

Still missing

• Confirm whether ENIGMA assigns a specific PVS1(RNA) strength for BRCA1 c.212+3A>G based on the available RNA evidence and Figure 1B/Appendix E guidance.

Sources

Rule

PS1 for splicing depends on demonstrating the same predicted impact on splicing as a previously classified pathogenic or likely pathogenic variant, with weight based on relative position and confidence of the reference variant.

Evidence considered

• Pathogenic splice donor variants at the same BRCA1 exon 5 donor region are present in the ENIGMA materials.
• Exact PS1 strength for this noncanonical +3 variant was not directly retrievable from the available rule extracts.

Still missing

• Confirm ENIGMA Table 5 positional weighting for noncanonical donor variants with similar splice outcomes to known pathogenic variants.

Sources

Rule

ENIGMA PM3 is reserved for BRCA1/2-related Fanconi anemia with scoring based on proband evidence.

Evidence considered

• No relevant recessive-disease or phase evidence was identified.

Still missing

• Fanconi anemia phenotype and phase data would be needed to assess PM3.

Sources

Rule

PP1 requires quantitative co-segregation evidence meeting the specified likelihood-ratio thresholds.

Evidence considered

• No variant-specific segregation LR meeting ENIGMA thresholds was identified.

Still missing

• A pedigree-based quantitative segregation analysis would be needed to assess PP1.

Sources

Rule

ENIGMA BS2 requires proband-level evidence scored under the BRCA1/2-related Fanconi anemia framework.

Evidence considered

• No qualifying BS2 point-based evidence was identified.

Still missing

• Phenotyped proband-level evidence would be needed to score BS2.

Sources

Rule

BS4 requires quantitative lack-of-segregation evidence meeting the specified likelihood-ratio thresholds.

Evidence considered

• No variant-specific benign-direction segregation LR was identified.

Still missing

• A pedigree-based quantitative segregation analysis supporting nonsegregation would be needed to assess BS4.

Sources