Variant classification summary

NM_007294.4:c.2998_3003del

BRCA1 · NP_009225.1:p.(Glu1000_Glu1001del) · NM_007294.4

GRCh37: chr17:41244544 TTTCCTC>T · GRCh38: chr17:43092527 TTTCCTC>T

Gene: BRCA1 Transcript: NM_007294.4

Final call

Likely Benign

BP1 strong benign BS1 supporting benign

Variant details

Gene

BRCA1

Transcript

NM_007294.4

Protein

NP_009225.1:p.(Glu1000_Glu1001del)

gnomAD AF

3.965347816766234e-05 (v4.1)

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_007294.4:c.2998_3003del is an in-frame deletion of 6 nucleotides in BRCA1 exon 10 resulting in deletion of two glutamic acid residues at positions 1000-1001 (p.Glu1000_Glu1001del). This is not a null variant; PVS1 does not apply.

2

The variant is present in gnomAD at low frequency: 5/282,204 alleles in v2.1 (AF=0.00177%) and 64/1,613,982 alleles in v4.1 (AF=0.00397%), with a maximum filter allele frequency of 0.0041%. This meets ENIGMA BS1_Supporting (FAF >0.002% and ≤0.01%).

3

The deletion is located at amino acid positions 1000-1001, outside the three ENIGMA-defined clinically important functional domains (RING aa 2-101, coiled-coil aa 1391-1424, BRCT aa 1650-1857). SpliceAI predicts no splicing impact (max delta = 0.01). This meets ENIGMA BP1_Strong for an in-frame deletion outside functional domains with no splicing predicted.

4

Clinical-history likelihood ratio from Li et al. 2020 (PMID:31853058) is 0.545 based on 7 probands, falling in the neutral zone. Neither PP4 nor BP5 is applied.

5

The variant was reported as a variant of unknown significance in 1 of 258 ovarian cancer patients by Smith et al. 2001 (PMID:11733976), identified in the RAD51-binding region of BRCA1. This observation alone does not meet any pathogenic criterion threshold.

6

Overall classification: Likely Benign. Using the ENIGMA point system: BP1_Strong (-4) + BS1_Supporting (-1) = -5 points, which falls in the Likely Benign range (-6 to -2). No pathogenic criteria are met.

Final determination: 1 Strong (Benign) criterion (BP1) plus 1 Supporting (Benign) criterion (BS1) yields Likely Benign per ENIGMA BRCA1 v1.2.0 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	Not met	NM_007294.4:c.2998_3003del is an in-frame 6-bp deletion resulting in p.(Glu1000_Glu1001del). PVS1 under ENIGMA BRCA1 v1.2.0 applies exclusively to null variants (nonsense, frameshift, canonical splice ±1,2, initiation codon, or single/multi-exon deletion). This in-frame deletion does not introduce a premature termination codon or alter the reading frame and is not assigned PVS1 in the ENIGMA Table 4 exon-level decision matrix for BRCA1 exon 10(11).	vcep_specifications_table4_v1_2_2024_11_18 cspec
PS1	N/A	PS1 under ENIGMA addresses predicted missense substitutions or splicing variants with same impact as a known pathogenic variant. This is an in-frame deletion, not a missense substitution or splicing variant.	cspec
PS2	N/A	PS2 is Not Applicable under ENIGMA BRCA1 v1.2.0.	cspec
PS3	Not met	No variant-specific functional evidence demonstrating a damaging effect was identified. ENIGMA Table 9 curated functional assay results are limited to missense and synonymous variants. The variant was not found in the ENIGMA Supplementary Table 4 functional assay dataset. OncoKB reports Unknown Oncogenic Effect with no variant-specific reviewed functional evidence.	vcep_specifications_table9_v1_2_2024_11_18 vcep_supplementarytables_v1_2_2024_11_18 oncokb
PS4	Not met	ENIGMA PS4 requires case-control study with p≤0.05 and OR≥4 (lower CI excludes 2.0). No case-control data are available for this variant. The variant has been observed in 1 ovarian cancer proband (Smith et al. 2001, PMID:11733976) as a VUS, which is insufficient to meet PS4 thresholds.	cspec PMID:11733976
PS5	N/A	PS5 is not a standard ACMG/AMP criterion and is not defined in the ENIGMA BRCA1 v1.2.0 specification.
PM1	N/A	PM1 is Not Applicable under ENIGMA BRCA1 v1.2.0. Captured by bioinformatic tool prediction and domain analysis per CSPEC.	cspec
PM2	Not met	ENIGMA PM2_Supporting requires absence from gnomAD v2.1 (non-cancer, exome only) and gnomAD v3.1/v4.1 (non-cancer). This variant is present in gnomAD: 5/282,204 alleles in v2.1 (AF=0.00177%) and 64/1,613,982 alleles in v4.1 (AF=0.00397%), with highest frequency in European (non-Finnish) population (v4.1 NFE AF=0.00517%). Therefore PM2 is not met.	gnomad_v2 gnomad_v4
PM4	N/A	PM4 is Not Applicable under ENIGMA BRCA1 v1.2.0.	cspec
PM5	N/A	Under ENIGMA BRCA1 v1.2.0, PM5 is repurposed for protein termination codon (PTC) variants in an exon where a proven pathogenic PTC has been seen before (PM5_PTC). This variant is an in-frame deletion, not a PTC, and does not introduce a stop codon. Classic same-residue missense PM5 is not applicable to deletions.	vcep_specifications_table4_v1_2_2024_11_18 cspec
PM6	N/A	PM6 is Not Applicable under ENIGMA BRCA1 v1.2.0.	cspec
PP1	Not met	No co-segregation data are available for this variant. ENIGMA PP1 requires quantitative co-segregation analysis with LR≥2.08 for Supporting.	cspec
PP2	N/A	PP2 is Not Applicable under ENIGMA BRCA1 v1.2.0.	cspec
PP3	Not met	ENIGMA PP3 requires the variant to be a missense or in-frame insertion/deletion/delins variant inside a clinically important functional domain (RING aa 2-101, coiled-coil aa 1391-1424, or BRCT aa 1650-1857) with BayesDel no-AF score ≥0.28, OR SpliceAI ≥0.2 for splicing prediction. The p.Glu1000_Glu1001del deletion is at positions 1000-1001, which is outside all three ENIGMA-defined functional domains. SpliceAI max delta score is 0.01 (no splicing impact). BayesDel/REVEL are not applicable to non-SNV variants. PP3 is not met.	cspec spliceai
PP4	Not met	ENIGMA PP4 is based on clinical-history likelihood ratio from Li et al. 2020 (PMID:31853058). The LR for c.2998_3003delGAGGAA is 0.545 (LOG(LR) = -0.607, N=7 probands), which falls in the neutral zone (>0.48 and <2.08). Per ENIGMA rules, PP4/BP5 is not applied when the LR is in the neutral range.	vcep_pmid_31853058_brca1_clinical_history_lr PMID:31853058
PP5	N/A	PP5 is Not Applicable under ENIGMA BRCA1 v1.2.0.	cspec
BA1	Not met	ENIGMA BA1 (Stand Alone) requires filter allele frequency (FAF) above 0.1% (FAF > 0.001) in gnomAD v2.1 (non-cancer, exome only) and/or gnomAD v3.1/v4.1 (non-cancer). Maximum FAF is 4.101e-05 (0.0041%) in gnomAD v4.1, well below the 0.1% threshold.	gnomad_v2 gnomad_v4
BS1	Met	ENIGMA BS1_Supporting applies when filter allele frequency (FAF) is above 0.002% (FAF > 0.00002) and ≤ 0.01% (FAF ≤ 0.0001) in gnomAD v2.1 and/or v3.1/v4.1 non-cancer, non-founder populations. The maximum FAF is 4.101e-05 (0.0041%) in gnomAD v4.1, which falls within the BS1_Supporting range (>0.002%, ≤0.01%). The variant is observed in 5/282,204 alleles in v2.1 and 64/1,613,982 alleles in v4.1, with highest frequency in the European (non-Finnish) population (v4.1 NFE AF=0.00517%).	gnomad_v2 gnomad_v4 cspec
BS2	Not met	ENIGMA BS2 requires observation in a homozygous state, in trans with a pathogenic variant, or in cis with a pathogenic variant in the absence of Fanconi anemia phenotype. No such data are available for this variant.	cspec
BS3	Not met	No variant-specific well-established functional studies demonstrating no damaging effect on protein function were identified. ENIGMA Table 9 curated functional assay results cover missense and synonymous variants only. The variant was not identified in the ENIGMA Supplementary Table 4 functional assay dataset.	vcep_specifications_table9_v1_2_2024_11_18 vcep_supplementarytables_v1_2_2024_11_18
BS4	Not met	No segregation data are available to assess lack of segregation. ENIGMA BS4 requires quantitative co-segregation analysis with LR ≤ 0.48 for Supporting.	cspec
BP1	Met	ENIGMA BP1_Strong applies to in-frame deletions outside a clinically important functional domain with no splicing predicted (SpliceAI ≤ 0.1). The p.Glu1000_Glu1001del deletion is at positions 1000-1001, which is outside the three ENIGMA-defined clinically important functional domains: RING (aa 2-101), coiled-coil (aa 1391-1424), and BRCT (aa 1650-1857). SpliceAI max delta score is 0.01, indicating no predicted splicing impact.	cspec spliceai
BP2	N/A	BP2 is Not Applicable under ENIGMA BRCA1 v1.2.0.	cspec
BP3	N/A	BP3 is Not Applicable under ENIGMA BRCA1 v1.2.0. Captured by bioinformatic tool prediction and domain analysis.	cspec
BP4	Not met	ENIGMA BP4 requires the variant to be a missense or in-frame insertion/deletion/delins variant inside a clinically important functional domain with no predicted impact (BayesDel ≤ 0.15 and SpliceAI ≤ 0.1). The p.Glu1000_Glu1001del deletion is outside the ENIGMA-defined functional domains (RING, coiled-coil, BRCT), so BP4 is not applicable.	cspec spliceai
BP5	Not met	ENIGMA BP5 is based on clinical-history likelihood ratio from Li et al. 2020 (PMID:31853058). The LR for c.2998_3003delGAGGAA is 0.545, which falls in the neutral zone (>0.48 and <2.08). Per ENIGMA rules, PP4/BP5 is not applied when the LR is in the neutral range.	vcep_pmid_31853058_brca1_clinical_history_lr PMID:31853058
BP6	N/A	BP6 is Not Applicable under ENIGMA BRCA1 v1.2.0.	cspec
BP7	Not met	ENIGMA BP7_Strong (RNA) requires well-established in vitro/in vivo functional studies showing no damaging effect as measured by mRNA transcript profile. BP7_Supporting applies to silent variants inside functional domains or intronic variants outside conserved splice motifs. This is an in-frame deletion with no mRNA assay data available, and it does not qualify for BP7_Supporting (not a silent or intronic variant).	cspec

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