BCL2 p.Phe153=
c.459C>T · rs137945099 · VCV709183
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.114%, 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 3.3 | GERP 2.8, phastCons 1 |
| Overall | ||
| CADD | 12.91 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.114%
European (non-Finnish) · 1,349/1,180,024 alleles
Filtering AF
0.109%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.107%
Overall
0.0885%
1,429/1,614,012 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.114% | 875 |
| Remaining individualsnot grpmax-eligible | 0.048% | 2,083 |
| Finnishnot grpmax-eligible | 0.0406% | 2,462 |
| African / African-American | 0.0174% | 5,762 |
| Admixed American | 0.0167% | 6,000 |
| East Asian | 0.00223% | 44,892 |
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
- BCL2
- Protein
- p.Phe153=
- Coding
- c.459C>T
- MANE Select
- NM_000633
- dbSNP
- rs137945099
- Type
- single nucleotide variant
- Location
- chr18:63318208 (GRCh38)
- Gene constraint
- LOEUF 0.368 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 74.21 · 63 PDB
- Residue 153
- an α-helix
Similar variants
- BCL2 p.Phe153Tyr Uncertain significance ★ ⚠ same residue
- BCL2 p.Ala113Asp Uncertain significance ★ ⚠ same type
- BCL2 p.Gly79Asp Uncertain significance ★ ⚠ same type
- BCL2 p.Met166Leu Uncertain significance ★ ⚠ same type
- BCL2 p.Phe150Leu Uncertain significance ★ ⚠ same type
- BCL2 p.Ser24Leu Uncertain significance ★ ⚠ same type
- BCL2 p.Ala100= Benign same type
- BCL2 p.Thr7= Benign 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/bcl2-p-phe153 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown