TFRC p.Phe650=
c.1950C>T · rs770264782 · VCV1669110
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0495%, 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 2.3 | GERP -2.9, phastCons 1 |
| Overall | ||
| CADD | 8.42 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0495%
Middle Eastern · 3/6,062 alleles
Filtering AF
0.0134%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00718%
Overall
0.00239%
35/1,461,870 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0495% | 2,021 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,835 |
| European (non-Finnish) | 0.00237% | 42,144 |
| South Asian | 0.0011% | 91,086 |
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
- TFRC
- Protein
- p.Phe650=
- Coding
- c.1950C>T
- MANE Select
- NM_001128148
- dbSNP
- rs770264782
- Type
- single nucleotide variant
- Location
- chr3:196053508 (GRCh38)
- Gene constraint
- LOEUF 0.489 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 86.87 · 24 PDB
- Residue 650
- an α-helix; the 'ligand-binding' region
Similar variants
- TFRC c.1678-3C>T Uncertain significance ★★ same type
- TFRC p.Ala166Val Uncertain significance ★★ ⚠ same type
- TFRC p.Ala196Thr Uncertain significance ★★ ⚠ same type
- TFRC p.Ala293Thr Uncertain significance ★★ ⚠ same type
- TFRC p.Ala540Val Uncertain significance ★★ ⚠ same type
- TFRC p.Ala72Ser Uncertain significance ★★ ⚠ same type
- TFRC p.Arg155His Uncertain significance ★★ ⚠ same type
- TFRC p.Arg155Pro 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/tfrc-p-phe650 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown