HBB p.Val55=
c.165T>C · rs760975738 · VCV799058
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0134%, eas)
Conditions
1
Inborn genetic diseases
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 -3.1 | GERP -3.7 |
| Overall | ||
| CADD | 2.121 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0134%
East Asian · 6/44,894 alleles
Filtering AF
0.00579%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00394%
Overall
0.000496%
8/1,614,030 alleles · ultra-rare
exomes 7/1,461,876 · genomes 1/152,154 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0134% | 7,482 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,243 |
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
- HBB
- Protein
- p.Val55=
- Coding
- c.165T>C
- MANE Select
- NM_000518
- dbSNP
- rs760975738
- Type
- single nucleotide variant
- Location
- chr11:5226727 (GRCh38)
- Gene constraint
- LOEUF 1.964 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 97.09 · 350 PDB
- Residue 55
- a UniProt-annotated variant site (in jacksonville; o(2) affinity up; unstable); an α-helix; the globin domain
Similar variants
- HBB p.Val55Ala Uncertain significance ★ ⚠ same residue
- HBB p.Val55Ile Uncertain significance ★ ⚠ same residue
- HBB p.His64Tyr Pathogenic/Likely pathogenic ★★ same condition
- HBB p.Val55fs Pathogenic ★★ same residue
- HBB p.His144= Benign/Likely benign ★★ same condition
- HBB p.Leu82= Likely benign ★★ same condition
- HBB p.Lys60= Likely benign ★★ same condition
- HBB p.Ala11= Conflicting classifications of pathogenicity ★ same condition
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/hbb-p-val55 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown