BCL11B p.Arg620=
c.1860C>T · rs556840516 · VCV1927852
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0354%, mid)
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 -0.29 | GERP -3.2, phastCons 0.049 |
| Overall | ||
| CADD | 10.87 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0354%
Middle Eastern · 2/5,654 alleles
Filtering AF
0.00621%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00256%
Overall
0.0016%
25/1,564,002 alleles · ultra-rare
exomes 22/1,413,562 · genomes 3/150,440 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0354% | 2,827 |
| African / African-American | 0.00837% | 11,951 |
| South Asian | 0.00565% | 17,709 |
| Remaining individualsnot grpmax-eligible | 0.00332% | 30,147 |
| Admixed American | 0.00173% | 57,816 |
| European (non-Finnish) | 0.000774% | 129,198 |
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
- BCL11B
- Protein
- p.Arg620=
- Coding
- c.1860C>T
- MANE Select
- NM_138576
- dbSNP
- rs556840516
- Type
- single nucleotide variant
- Location
- chr14:99174976 (GRCh38)
- Gene constraint
- LOEUF 0.462 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 51.76 · 6 PDB
- Residue 620
- a UniProt-annotated variant site (in iddsfta)
Similar variants
- BCL11B p.Arg620Cys Uncertain significance ★★ ⚠ same residue
- BCL11B p.Asn807Lys Pathogenic/Likely pathogenic ★★ ⚠ same type
- BCL11B p.Cys808Arg Likely pathogenic ★★ same type
- BCL11B p.Tyr824Ter Likely pathogenic ★★ same type
- BCL11B p.Ala152Val Uncertain significance ★★ ⚠ same type
- BCL11B p.Ala188Thr Uncertain significance ★★ ⚠ same type
- BCL11B p.Ala339Val Uncertain significance ★★ ⚠ same type
- BCL11B p.Ala424Asp 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/bcl11b-p-arg620 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown