Variant classification summary

NM_007294.4:c.4935G>C

BRCA1 · NP_009225.1:p.(Arg1645Ser) · NM_007294.4

GRCh37: chr17:41222996 C>G · GRCh38: chr17:43070979 C>G

Gene: BRCA1 Transcript: NM_007294.4

Final call

Benign

BS3 strong BP1 strong PM2 supporting

Variant details

Gene

BRCA1

Transcript

NM_007294.4

Protein

NP_009225.1:p.(Arg1645Ser)

gnomAD AF

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

c.4935G>C (p.Arg1645Ser) is a missense variant in BRCA1 exon 15, located at amino acid position 1645, five residues N-terminal to the BRCT domain (aa 1650-1857).

2

ENIGMA BRCA1 VCEP Table 9 assigns BS3 (Strong) to this variant based on two calibrated functional studies demonstrating protein function indistinguishable from benign control variants (Findlay 2018, PMID:30209399; Fernandes 2019, PMID:30765603).

3

ENIGMA BP1_Strong applies because the variant is a missense substitution located outside all clinically important functional domains (RING aa 2-101, coiled-coil aa 1391-1424, BRCT aa 1650-1857) with no predicted splicing impact (SpliceAI max delta 0.02).

4

PM2_Supporting is met because the variant is absent from gnomAD v2.1 and v4.1 in outbred populations.

5

Per ENIGMA Table 3 combining rules, two Strong Benign criteria (BS3 + BP1) meet the threshold for Benign classification. The single Supporting Pathogenic criterion (PM2) does not alter the classification.

6

Final classification: Benign.

Final determination: ENIGMA BRCA1/BRCA2 v1.2 Table 3 conflicting-evidence point system: total score of -7 (BS3 Strong -4, BP1 Strong -4, PM2 Supporting +1) meets the Benign threshold (<= -7); two Strong benign criteria also independently satisfy the non-conflicting Benign combination rule.

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	Missense substitution (p.Arg1645Ser); PVS1 is restricted to null variants (nonsense, frameshift, canonical splice, initiation codon, exon deletion) per ENIGMA BRCA1 specification v1.2.
PS1	Not met	No pathogenic missense variant has been established at residue Arg1645. All other missense substitutions at this residue (R1645G, R1645K, R1645T) are assigned BS3 (benign functional evidence) by ENIGMA Table 9, precluding a pathogenic comparator for PS1.	vcep_specifications_table9_v1_2_2024_11_18
PS2	N/A	ENIGMA BRCA1 VCEP v1.2 deems PS2 not applicable for BRCA1/2.	cspec
PS3	Not met	ENIGMA Table 9 assigns BS3 (Strong) to c.4935G>C based on two calibrated functional studies (Findlay 2018 PMID:30209399, Fernandes 2019 PMID:30765603) showing protein function similar to benign control variants. ST4 functional assay also reports 'No functional impact' with FUNC classification. No evidence of damaging effect exists for this variant.	vcep_specifications_table9_v1_2_2024_11_18 PMID:30209399 PMID:30765603
PS4	Not assessed	No case-control study with odds ratio and p-value is available for this variant. The variant has been observed in ClinVar and listed as a VUS in one Japanese HBOC cohort study (Arai 2018, PMID:29176636, n=1), but this does not meet the ENIGMA PS4 threshold (OR >=4, p<=0.05).	PMID:29176636
PS5	Not met	No pathogenic missense variant has been established at residue Arg1645. All other substitutions at this residue are classified as BS3 (benign functional evidence) by ENIGMA Table 9. PS5 requires a previously established pathogenic variant at the same residue.	vcep_specifications_table9_v1_2_2024_11_18
PM1	N/A	ENIGMA BRCA1 VCEP v1.2 explicitly states PM1 is not applicable; considered as a component of bioinformatic analysis under PP3/BP4.	cspec
PM2	Met	Variant is absent from gnomAD v2.1 (exome, non-cancer) and gnomAD v4.1 (non-cancer). Per ENIGMA v1.2, PM2_Supporting applies when a variant is absent from controls in outbred populations (read depth >=25 assumed per pipeline).	gnomad_v2 gnomad_v4
PM5	N/A	ENIGMA BRCA1 VCEP v1.2 repurposes PM5 exclusively for protein termination codon (PTC) variants in exons where a proven pathogenic PTC has been observed. This is a missense variant and does not qualify for PM5_PTC logic.	cspec
PM6	N/A	ENIGMA BRCA1 VCEP v1.2 deems PM6 not applicable; BRCA1/2-related cancers occur relatively commonly and de novo occurrence cannot be calibrated.	cspec
PP1	Not assessed	No co-segregation data or likelihood ratio analysis is available for this variant. ENIGMA PP1 requires quantitative co-segregation analysis (LR >=2.08 for Supporting).
PP2	N/A	ENIGMA BRCA1 VCEP v1.2 deems PP2 not applicable.	cspec
PP3	Not met	PP3 for missense variants requires location inside a clinically important functional domain AND BayesDel no-AF score >=0.28. Arg1645 is at position 1645, which is outside the BRCT domain (aa 1650-1857). Additionally, BayesDel score is -0.0818436, which is far below the 0.28 threshold. SpliceAI max delta is 0.02, below the 0.2 threshold for splicing-based PP3.	bayesdel spliceai
PP4	Not met	Variant is not present in the Li et al. 2020 (PMID:31853058) BRCA1 clinical-history likelihood ratio table. No PP4 LR data is available for this variant.	PMID:31853058
PP5	N/A	ENIGMA BRCA1 VCEP v1.2 deems PP5 not applicable per ClinGen Sequence Variant Interpretation VCEP Review Committee recommendation.	cspec
BA1	Not met	Variant is absent from gnomAD v2.1 and v4.1. ENIGMA BA1 requires filter allele frequency (FAF) >0.1% in a non-founder population. Not met.	gnomad_v2 gnomad_v4
BS1	Not met	Variant is absent from gnomAD v2.1 and v4.1. ENIGMA BS1 Strong requires FAF >0.01%; BS1 Supporting requires FAF >0.002%. Not met.	gnomad_v2 gnomad_v4
BS2	Not assessed	No proband-level co-occurrence data or data on observation in healthy adults without Fanconi Anemia phenotype is available for this variant. ENIGMA BS2 requires point-based scoring per Specifications Table 8.
BS3	Met	ENIGMA Table 9 assigns BS3 (Strong) to c.4935G>C (p.Arg1645Ser). Two calibrated functional studies demonstrate protein function similar to benign control variants: Findlay et al. 2018 (PMID:30209399, saturation genome editing, classification: FUNC) and Fernandes et al. 2019 (PMID:30765603, BRCT domain functional assay, classification: Not Pathogenic). ST4 confirms no functional impact with FUNC classification.	vcep_specifications_table9_v1_2_2024_11_18 PMID:30209399 PMID:30765603
BS4	Not assessed	No segregation data or likelihood ratio analysis is available for this variant. ENIGMA BS4 requires quantitative co-segregation analysis showing lack of segregation (LR <=0.48 for Supporting).
BP1	Met	ENIGMA BP1_Strong applies to missense variants located outside a clinically important functional domain with no splicing predicted. Arg1645 (position 1645) lies outside all three BRCA1 functional domains (RING aa 2-101, coiled-coil aa 1391-1424, BRCT aa 1650-1857). SpliceAI max delta is 0.02 (<=0.1), predicting no splicing impact.	cspec spliceai
BP2	N/A	ENIGMA BRCA1 VCEP v1.2 deems BP2 not applicable; applied only in the context of BS2.	cspec
BP4	Not met	ENIGMA BP4 for missense variants explicitly requires location inside a clinically important functional domain with BayesDel <=0.15 and SpliceAI <=0.1. Arg1645 is outside the BRCT domain (aa 1650-1857), so the protein-change BP4 rule does not apply. SpliceAI is 0.02 but the splicing-based BP4 rule targets intronic variants outside donor/acceptor sites, not exonic missense.	cspec bayesdel spliceai
BP5	Not assessed	Variant is not present in the Li et al. 2020 (PMID:31853058) BRCA1 clinical-history likelihood ratio table. No BP5 LR data is available for this variant.	PMID:31853058
BP6	N/A	ENIGMA BRCA1 VCEP v1.2 deems BP6 not applicable per ClinGen Sequence Variant Interpretation VCEP Review Committee recommendation.	cspec
BP7	Not assessed	No mRNA splicing assay data is available for this variant. ENIGMA BP7 requires well-established mRNA transcript profile data. SpliceAI predicts no splicing impact (delta 0.02), but BP7_Strong (RNA) requires direct mRNA assay evidence, not in silico prediction alone.	spliceai

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