LYFE Sciences · Project HERA
Variant Interpretation · Classification Report
Generated: 2026-04-26
Case ID: NM_000059.4_c.663T_G_20260426_192223
Framework: ACMG/AMP 2015 with ENIGMA Table 3 adaptations
Variant classification summary

NM_000059.4:c.663T>G

BRCA2  · NP_000050.3:p.(Phe221Leu)  · NM_000059.4
GRCh37: chr13:32903611 T>G  ·  GRCh38: chr13:32329474 T>G
Gene: BRCA2 Transcript: NM_000059.4
Final call
BP1_Strong BP6_Supporting
All criteria require review: For research and educational purposes only.
Variant details
Gene
BRCA2
Transcript
NM_000059.4
Protein
NP_000050.3:p.(Phe221Leu)
gnomAD AF
ClinVar
OncoKB
Unknown Oncogenic Effect
Classification rationale
Interpretation summary
Generated evidence synthesis
1
The BRCA2 c.663T>G (p.Phe221Leu, p.F221L) variant has not been observed in somatic cancers in COSMIC and has been reported in ClinVar, where the ClinGen ENIGMA BRCA1/2 expert panel classified it as likely benign.
2
This variant is present at very low frequency in population databases, including gnomAD v2.1 at 1/245048 alleles (AF 4.08e-06) and gnomAD v4.1 at 5/1598264 alleles (AF 3.13e-06; grpmax FAF 4.45e-06), which is below ENIGMA BS1/BA1 thresholds and means the variant is not absent from controls for PM2_Supporting.
3
No calibrated ENIGMA functional assay result for this specific variant was identified in the curated BRCA2 functional dataset, so functional evidence was not applied.
4
This missense change occurs outside the BRCA2 PALB2-binding and DNA-binding domains used for ENIGMA missense protein interpretation, and SpliceAI predicts no significant splice effect with a maximum delta score of 0.01, supporting BP1_Strong.
Final determination: Likely benign based on one strong benign criterion and one supporting benign criterion under the ENIGMA BRCA1/BRCA2 Table 3 combination rules.
Criteria assessment
ACMG/AMP criteria review
Criteria shown when status is available
All criteria require review: For research and educational purposes only.
Criterion Status Rationale Evidence used
PVS1 N/A This missense variant, NM_000059.4:c.663T>G (p.Phe221Leu, p.F221L), does not fall into the BRCA2 PVS1 null-variant categories, and no RNA study demonstrating a pathogenic transcript effect was identified. Available evidence therefore does not support application of PVS1.
cspec pvs1_gene_context pvs1_variant_assessment
PS1 Not assessed No same-amino-acid pathogenic or likely pathogenic BRCA2 variant acting through the same predicted mechanism was identified from the available evidence, so PS1 was not assessed.
cspec clinvar spliceai
PS2 N/A De novo evidence is not part of the ENIGMA BRCA2 framework for this review, so PS2 is not applicable.
cspec
PS3 Not assessed No calibrated BRCA2 functional assay result for this specific variant was identified in the curated ENIGMA functional dataset, so PS3 was not assessed.
cspec vcep_specifications_table9_v1_2_2024_11_18
PS4 Not met Available evidence does not show a statistically significant enrichment of this variant in affected individuals compared with controls. No case-control result meeting the ENIGMA PS4 threshold of p-value ≤0.05 and odds ratio ≥4 was identified.
cspec vcep_humu_40_1557_s001 PMID:31131967
PM1 N/A PM1 is not applicable in the ENIGMA BRCA2 specification.
cspec
PM2 Not met This variant is not absent from population databases. It is present in gnomAD v2.1 at 1/245048 alleles (AF 4.08e-06) and in gnomAD v4.1 at 5/1598264 alleles (AF 3.13e-06), so it does not meet the ENIGMA PM2_Supporting requirement for absence from controls.
cspec gnomad_v2 gnomad_v4
PM3 Not assessed No evidence was identified for biallelic BRCA2 disease, Fanconi anemia phenotype, or qualifying trans observations for this variant, so PM3 was not assessed.
cspec
PM4 N/A PM4 is not applicable in the ENIGMA BRCA2 specification.
cspec
PM5 N/A In the ENIGMA BRCA2 specification, PM5 is used for protein-terminating variants in eligible exons. This variant is missense, so PM5 is not applicable.
cspec vcep_specifications_table4_v1_2_2024_11_18
PM6 N/A PM6 is not applicable in the ENIGMA BRCA2 specification.
cspec
PP1 Not assessed No quantitative co-segregation result was identified for this variant, so PP1 was not assessed.
cspec vcep_humu_40_1557_s001
PP2 N/A PP2 is not applicable in the ENIGMA BRCA2 specification.
cspec
PP3 Not met Available predictive evidence does not support PP3. This missense variant lies outside the BRCA2 clinically important domains used for PP3 protein-based application, and SpliceAI predicts no significant splice effect with a max delta score of 0.01, which is below the ENIGMA PP3 splice threshold of 0.20.
cspec spliceai
PP4 Not met The BRCA2 clinical-history likelihood ratio for this variant is 0.67 in 6 probands, which is below the ENIGMA PP4 threshold of 2.08. Available evidence therefore does not support PP4.
cspec vcep_pmid_31853058_brca2_clinical_history_lr PMID:31853058
PP5 N/A PP5 is not applicable in the ENIGMA BRCA2 specification.
cspec
BA1 Not met This variant does not reach the ENIGMA BA1 threshold. The highest available group maximum filtering allele frequency is 4.45e-06 in gnomAD v4.1, which is below the BA1 threshold of 0.001.
cspec gnomad_v4 gnomad_v2
BS1 Not met Population frequency is below the ENIGMA BS1 thresholds. The highest available group maximum filtering allele frequency is 4.45e-06 in gnomAD v4.1, which is below the BS1_Supporting threshold of 0.00002 and the BS1 threshold of 0.0001, so BS1 is not met.
cspec gnomad_v4 gnomad_v2
BS2 Not assessed No point-based evidence was identified showing this variant in individuals without features of BRCA2-related Fanconi anemia, so BS2 was not assessed.
cspec
BS3 Not assessed No calibrated benign functional assay result for this specific variant was identified in the curated ENIGMA functional dataset, so BS3 was not assessed.
cspec vcep_specifications_table9_v1_2_2024_11_18
BS4 Not assessed No quantitative lack-of-segregation likelihood ratio was identified for this variant, so BS4 was not assessed.
cspec vcep_humu_40_1557_s001
BP1 Met This missense variant affects codon 221, which is outside the BRCA2 clinically important domains used by ENIGMA, and SpliceAI predicts no significant splice effect with a max delta score of 0.01, which is below the no-splicing threshold of 0.10. This supports BP1_Strong.
cspec spliceai
BP2 N/A BP2 is not applicable in the ENIGMA BRCA2 specification.
cspec
BP3 N/A BP3 is not applicable in the ENIGMA BRCA2 specification.
cspec
BP4 N/A For BRCA2 missense variants, the ENIGMA BP4 protein-based rule is used for variants inside clinically important domains with benign predictions. This variant is outside those domains, so BP4 is not the appropriate rule for this observation and BP1_Strong is used instead.
cspec spliceai
BP5 Not met The BRCA2 clinical-history likelihood ratio for this variant is 0.67 in 6 probands, which is above the ENIGMA BP5 threshold of 0.48. This value is in the neutral zone, so BP5 is not met.
cspec vcep_pmid_31853058_brca2_clinical_history_lr PMID:31853058
BP6 Met Expert panel ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen classified as Likely benign.
cspec clinvar
BP7 N/A This is a missense variant rather than a synonymous or qualifying intronic variant, so BP7 is not applicable.
cspec
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