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.

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.

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.

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

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.

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.

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.

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).

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.