Variant classification summary

NM_007294.3:c.5073A>G

BRCA1 · NP_009225.1:p.(Thr1691=) · NM_007294.3

GRCh37: chr17:41219626 T>C · GRCh38: chr17:43067609 T>C

Gene: BRCA1 Transcript: NM_007294.3

Final call

VUS

PM2 supporting PP3 supporting

Variant details

Gene

BRCA1

Transcript

NM_007294.3

Protein

NP_009225.1:p.(Thr1691=)

gnomAD AF

6.221164900685323e-07 (v4.1)

ClinVar

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_007294.3:c.5073A>G (p.Thr1691=) is a synonymous variant in exon 16 of BRCA1, located within the BRCT domain (aa 1650-1857), a clinically important functional domain.

2

The variant is absent from gnomAD v2.1 and is present at extremely low frequency in gnomAD v4.1 (1/1,607,416 alleles; AF=6.22e-7), meeting PM2_Supporting under ENIGMA population frequency criteria.

3

SpliceAI predicts a donor loss effect with a max delta score of 0.71 (DS_DL=0.71), exceeding the ENIGMA PP3 threshold of 0.2 for predicted splicing impact in silent variants, meeting PP3 at Supporting strength.

4

No case-control data (PS4), cosegregation evidence (PP1), or non-segregation evidence (BS4) were identified for this variant.

5

BP4 is not met because SpliceAI predicts splicing impact (0.71 > 0.1 threshold). BP1 is not applicable because the variant lies within the BRCT clinically important functional domain and has predicted splicing impact. BP7_Supporting is not met because BP4 is a prerequisite.

6

No functional assay data from calibrated studies were identified in ENIGMA Table 9 or ST4. The Findlay et al. 2018 (PMID:30209399) saturation genome editing study covers this region, but the variant-specific functional score could not be retrieved from the inaccessible full-text supplementary data, leaving PS3 and BS3 unassessed.

7

No clinical-history likelihood ratio data were available for this variant in the Li et al. 2020 (PMID:31853058) BRCA1 table, leaving PP4 and BP5 unassessed.

8

Applying the ENIGMA point-based classification system: PM2_Supporting (+1, pathogenic) + PP3_Supporting (+1, pathogenic) = +2 total. With no benign criteria met and only two pathogenic Supporting criteria, the total points (+2) fall within the VUS range (-1 to +5).

9

However, the SpliceAI prediction of donor loss (delta 0.71) suggests this synonymous variant may alter splicing, and definitive classification requires functional characterization via mRNA transcript analysis and/or retrieval of the Findlay et al. 2018 saturation genome editing functional score to resolve PS3/BS3.

Final determination: ENIGMA v1.2 point system: two pathogenic Supporting criteria (+2 total) fall within VUS range (-1 to +5); no ENIGMA Table 3 all_of combination or generic ACMG rule is satisfied by Supporting-only evidence.

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	NM_007294.3:c.5073A>G is a synonymous variant (p.Thr1691=). It is not a null variant (nonsense, frameshift, or canonical ±1,2 splice consensus change) and no mRNA assay data demonstrating a damaging effect on transcript profile is available for this specific variant to invoke PVS1(RNA). PVS1 does not apply.	pvs1_generic_framework cspec
PS1	Not assessed	No previously classified pathogenic or likely pathogenic comparator variant with the same predicted amino acid change or splicing impact at this residue was identified in available evidence sources. This is a synonymous variant, and ENIGMA PS1 rules for missense substitutions require a same-residue pathogenic missense comparator; PS1 for splicing impact requires a reference variant with the same predicted splicing consequence, which was not found.	cspec
PS2	N/A	ENIGMA BRCA1/2 specification v1.2 marks PS2 as Not Applicable.	cspec
PS3	Not assessed	The variant c.5073A>G is not listed in ENIGMA Table 9 (curated functional assay results) or Supplementary Table 4 (full functional assay dataset). Although the saturation genome editing study by Findlay et al. (PMID:30209399) covers the BRCA1 DNA binding domain and may include functional scores for this position, the full-text could not be accessed to verify the variant-specific functional score and determine whether it meets the calibrated thresholds for PS3 strength assignment.	cspec PMID:30209399
PS4	Not met	No case-control study demonstrating significantly increased prevalence of c.5073A>G in affected individuals versus controls (p≤0.05 and OR≥4) was identified. The variant is absent from ClinVar, and no published case-control data for this specific variant were found in the literature.	clinvar cspec
PS5	N/A	PS5 is not listed in the ENIGMA BRCA1/2 v1.2 specification criteria.	cspec
PM1	N/A	ENIGMA BRCA1/2 specification v1.2 marks PM1 as Not Applicable.	cspec
PM2	Met	The variant is absent from gnomAD v2.1 (non-cancer, exome subset) and is present at extremely low frequency in gnomAD v4.1 (1/1,607,416 alleles; AF=6.22e-7; no homozygotes). Under ENIGMA rules, PM2_Supporting applies when a variant is absent from gnomAD v2.1 and v3.1 non-cancer populations.	gnomad_v2 gnomad_v4 cspec
PM5	N/A	Under ENIGMA BRCA1/2 specification, PM5 is repurposed for PTC (protein termination codon) variants with PVS1 applied, to capture additional weight from proven pathogenic PTCs in the same exon. This variant is synonymous (p.Thr1691=), not a PTC, and PVS1 is not applicable. Classic same-residue missense PM5 is not operative under this framework.	cspec pm5_candidates
PM6	N/A	ENIGMA BRCA1/2 specification v1.2 marks PM6 as Not Applicable.	cspec
PP1	Not met	No cosegregation data were identified for c.5073A>G in any published study or database. No LOD score or quantitative cosegregation analysis meeting the ENIGMA LR thresholds (≥2.08 for Supporting) was found.	cspec
PP2	N/A	ENIGMA BRCA1/2 specification v1.2 marks PP2 as Not Applicable.	cspec
PP3	Met	SpliceAI predicts a splicing impact for this silent variant with a max delta score of 0.71 (donor loss: DS_DL=0.71, DP_DL=-1), exceeding the ENIGMA PP3 threshold of ≥0.2 for predicted splicing alterations. Under ENIGMA rules, PP3 at Supporting strength applies to silent variants with SpliceAI ≥0.2 irrespective of location within clinically important functional domains.	spliceai cspec
PP4	Not assessed	The variant c.5073A>G was not found in the Li et al. 2020 (PMID:31853058) BRCA1 clinical-history likelihood-ratio table. No clinical-history LR data is available to adjudicate PP4 under the ENIGMA multifactorial clinical data framework.	cspec PMID:31853058
PP5	N/A	ENIGMA BRCA1/2 specification v1.2 marks PP5 as Not Applicable.	cspec
BA1	Not met	ENIGMA BA1 requires a filter allele frequency (FAF) above 0.1% (FAF > 0.001) in gnomAD v2.1 or v3.1 non-cancer populations. The variant is absent from gnomAD v2.1 and has an allele frequency of 6.22e-7 (0.00006%) in gnomAD v4.1, well below the BA1 threshold.	gnomad_v2 gnomad_v4 cspec
BS1	Not met	ENIGMA BS1_Strong requires FAF > 0.01% and BS1_Supporting requires FAF > 0.002% and ≤ 0.01%. The variant has an allele frequency of 6.22e-7 (0.000062%) in gnomAD v4.1, which falls below both BS1 thresholds. The variant is absent from gnomAD v2.1.	gnomad_v2 gnomad_v4 cspec
BS2	Not assessed	No data were identified regarding observation of this variant in homozygous or compound heterozygous state in individuals without Fanconi anemia phenotype. BS2 under ENIGMA requires documented absence of recessive disease features in individuals with biallelic variants, which cannot be assessed from available evidence.	cspec
BS3	Not assessed	The variant c.5073A>G is not listed in ENIGMA Table 9 (curated functional assay results assigning BS3 codes) or Supplementary Table 4 (full functional assay dataset). While Findlay et al. 2018 (PMID:30209399) saturation genome editing assay covers all single nucleotide variants in the BRCA1 DNA binding domain including this position, the full-text supplementary data could not be accessed to retrieve the variant-specific functional score and determine whether it meets the calibrated benign functional threshold for BS3 assignment.	cspec PMID:30209399
BS4	Not met	No data demonstrating lack of segregation of c.5073A>G in affected family members were identified. No quantitative cosegregation analysis showing an LR meeting the ENIGMA BS4 thresholds (≤0.48 for Supporting) was found in the literature or databases.	cspec
BP1	N/A	ENIGMA BP1_Strong requires a silent substitution outside a clinically important functional domain AND no splicing predicted (SpliceAI ≤0.1). The variant c.5073A>G encodes p.Thr1691=, which lies within the BRCT domain (aa 1650-1857), a clinically important functional domain. Additionally, SpliceAI predicts splicing impact (max delta=0.71). Neither condition for BP1 is satisfied.	spliceai cspec
BP2	N/A	ENIGMA BRCA1/2 specification v1.2 marks BP2 as Not Applicable.	cspec
BP4	Not met	ENIGMA BP4_Supporting for a silent variant inside a clinically important functional domain requires no predicted splicing impact (SpliceAI ≤0.1). The variant is located within the BRCT domain (aa 1650-1857), and SpliceAI predicts a splicing alteration (max delta=0.71, exceeding 0.1). BP4 is therefore not met.	spliceai cspec
BP5	Not assessed	The variant c.5073A>G was not found in the Li et al. 2020 (PMID:31853058) BRCA1 clinical-history likelihood-ratio table. No clinical-history LR data is available to adjudicate BP5 under the ENIGMA multifactorial clinical data framework.	cspec PMID:31853058
BP6	N/A	ENIGMA BRCA1/2 specification v1.2 marks BP6 as Not Applicable.	cspec
BP7	Not met	ENIGMA BP7_Strong (RNA) requires a well-established mRNA assay showing no splicing aberration, which is not available for this variant. BP7_Supporting for silent variants inside a clinically important functional domain requires BP4 to be met first; since BP4 is not met (SpliceAI predicts splicing impact), BP7_Supporting cannot be applied.	cspec spliceai

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