CD1B p.Phe76=
c.228T>C · rs61747107 · VCV775615
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.51%, afr)
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 -3.8 | GERP -2.5 |
| Overall | ||
| CADD | 5.094 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.51%
African / African-American · 1,883/75,048 alleles
Filtering AF
2.41%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.38%
Overall
0.146%
2,354/1,614,088 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.51% | 40 |
| Admixed American | 0.302% | 332 |
| Remaining individualsnot grpmax-eligible | 0.214% | 466 |
| Middle Eastern | 0.165% | 606 |
| European (non-Finnish) | 0.012% | 8,309 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
| Finnishnot grpmax-eligible | 0.00312% | 32,021 |
| South Asian | 0.0011% | 91,080 |
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
- CD1B
- Protein
- p.Phe76=
- Coding
- c.228T>C
- MANE Select
- NM_001764
- dbSNP
- rs61747107
- Type
- single nucleotide variant
- Location
- chr1:158330896 (GRCh38)
- Gene constraint
- LOEUF 1.334 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.00 · 28 PDB
Similar variants
- CD1B p.Gly104Ser Benign ★★ same type
- CD1B p.Gly247Ser Benign ★★ ⚠ same type
- CD1C p.Arg283Thr Likely benign ★★ ⚠ same type
- CD1C p.Gln23= Benign ★★ same type
- CD1C p.Phe300Ser Benign ★★ same type
- CD1C p.Val282Leu Likely benign ★★ ⚠ same type
- CD1C p.Val318= Benign ★★ same type
- CD1B p.Ala10Thr 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/cd1b-p-phe76 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown