BCL9 p.Asn5=
c.15C>T · rs41299583 · VCV2639121
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0531%, 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 1, phastCons 1 |
| Overall | ||
| CADD | 8.837 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0531%
European (non-Finnish) · 627/1,180,038 alleles
Filtering AF
0.0497%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0483%
Overall
0.0434%
700/1,614,052 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0531% | 1,882 |
| Admixed American | 0.05% | 2,000 |
| Remaining individualsnot grpmax-eligible | 0.0448% | 2,232 |
| African / African-American | 0.0174% | 5,763 |
| Finnishnot grpmax-eligible | 0.00312% | 32,019 |
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
- BCL9
- Protein
- p.Asn5=
- Coding
- c.15C>T
- MANE Select
- NM_004326
- dbSNP
- rs41299583
- Type
- single nucleotide variant
- Location
- chr1:147611851 (GRCh38)
- Gene constraint
- LOEUF 0.374 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 43.07 · 8 PDB
- Residue 5
- the 'disordered' region
Similar variants
- BCL9 c.661-8G>T Benign/Likely benign ★★ same type
- BCL9 p.Arg485= Benign ★★ same type
- BCL9 p.Ala1042Thr Uncertain significance ★ ⚠ same type
- BCL9 p.Ala1190Val Uncertain significance ★ ⚠ same type
- BCL9 p.Ala1281Asp Uncertain significance ★ ⚠ same type
- BCL9 p.Ala128Pro Uncertain significance ★ ⚠ same type
- BCL9 p.Ala1337Val Uncertain significance ★ ⚠ same type
- BCL9 p.Ala1407Gly 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/bcl9-p-asn5 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown