BCL6 p.Pro245=
c.735G>A · VCV3480165
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.102%, 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 -9.3 | GERP -4.1 |
| Overall | ||
| CADD | 0.305 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.102%
European (non-Finnish) · 1,208/1,180,018 alleles
Filtering AF
0.0976%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0956%
Overall
0.0797%
1,287/1,614,138 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.102% | 977 |
| Admixed American | 0.0466% | 2,144 |
| Remaining individualsnot grpmax-eligible | 0.0464% | 2,155 |
| African / African-American | 0.0133% | 7,504 |
| East Asian | 0.0111% | 8,974 |
| Finnishnot grpmax-eligible | 0.0109% | 9,146 |
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
- BCL6
- Protein
- p.Pro245=
- Coding
- c.735G>A
- MANE Select
- NM_001706
- Type
- single nucleotide variant
- Location
- chr3:187729670 (GRCh38)
- Gene constraint
- LOEUF 0.221 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 52.89 · 222 PDB
Similar variants
- BCL6 p.Pro245Leu Uncertain significance ★ ⚠ same residue
- BCL6 c.1356-3T>C Likely benign ★★ same type
- BCL6 c.161+8A>T Benign ★★ same type
- BCL6 c.1840-7C>T Likely benign ★★ same type
- BCL6 p.Ser209= Benign ★★ same type
- BCL6 p.Thr48= Benign ★★ same type
- BCL6 p.Ala107Thr Uncertain significance ★ ⚠ same type
- BCL6 p.Ala291Thr 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/bcl6-p-pro245 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown