BCLAF1 p.Leu248=
c.744C>T · rs79123484 · VCV3024809
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0722%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.7 | GERP -0.43, phastCons 1 |
| Overall | ||
| CADD | 6.847 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0722%
European (non-Finnish) · 835/1,157,310 alleles
Filtering AF
0.0681%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0664%
Overall
0.0581%
920/1,583,494 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0722% | 1,386 |
| Finnishnot grpmax-eligible | 0.0685% | 1,460 |
| Remaining individualsnot grpmax-eligible | 0.0244% | 4,091 |
| Admixed American | 0.0188% | 5,309 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0177% | 5,664 |
| African / African-American | 0.0147% | 6,789 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- BCLAF1
- Protein
- p.Leu248=
- Coding
- c.744C>T
- MANE Select
- NM_014739
- dbSNP
- rs79123484
- Type
- single nucleotide variant
- Location
- chr6:136278137 (GRCh38)
- Gene constraint
- LOEUF 0.213 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 47.04 · 2 PDB
- Residue 248
- the 'disordered' region
Similar variants
- BCLAF1 p.Gly210Ser Benign/Likely benign ★★ same type
- BCLAF1 c.2397+1G>C Uncertain significance ★ same type
- BCLAF1 p.Ala169Thr Uncertain significance ★ ⚠ same type
- BCLAF1 p.Ala310Val Uncertain significance ★ ⚠ same type
- BCLAF1 p.Ala669Val Uncertain significance ★ ⚠ same type
- BCLAF1 p.Arg107Gln Uncertain significance ★ ⚠ same type
- BCLAF1 p.Arg111His Uncertain significance ★ ⚠ same type
- BCLAF1 p.Arg126Lys Uncertain significance ★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/bclaf1-p-leu248 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown