BCL10 p.Leu95=
c.285G>C · rs780017880 · VCV3038573
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0167%, amr)
Conditions
1
BCL10-related disorder
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 -0.7 | GERP -4.2, phastCons 0.008 |
| Overall | ||
| CADD | 5.064 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0167%
Admixed American · 10/59,830 alleles
Filtering AF
0.00902%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00683%
Overall
0.00105%
17/1,613,244 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0167% | 5,983 |
| European (non-Finnish) | 0.000593% | 168,540 |
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
- BCL10
- Protein
- p.Leu95=
- Coding
- c.285G>C
- MANE Select
- NM_003921
- dbSNP
- rs780017880
- Type
- single nucleotide variant
- Location
- chr1:85270679 (GRCh38)
- Gene constraint
- LOEUF 0.637 · pLI 0.73 (gnomAD)
- Structure
- AlphaFold pLDDT 70.43 · 5 PDB
- Residue 95
- the card domain; an α-helix
Disease context
BCL10-related disorder
Similar variants
- BCL10 p.Arg232Ter Uncertain significance ★★ same type
- BCL10 p.Arg87Gln Uncertain significance ★★ ⚠ same type
- BCL10 p.Cys119Tyr Uncertain significance ★★ ⚠ same type
- BCL10 p.Gln97Glu Uncertain significance ★★ ⚠ same type
- BCL10 p.Ile96Val Uncertain significance ★★ ⚠ same type
- BCL10 p.Leu177Ile Uncertain significance ★★ ⚠ same type
- BCL10 p.Thr162Met Uncertain significance ★★ ⚠ same type
- BCL10 p.Thr190Ala 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/bcl10-p-leu95 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown