TFRC p.Ser472=
c.1416G>A · rs776990727 · VCV2177105
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0189%, sas)
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 -1.2 | GERP -3.1 |
| Overall | ||
| CADD | 4.125 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0189%
South Asian · 17/90,016 alleles
Filtering AF
0.012%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00987%
Overall
0.00329%
53/1,609,274 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0189% | 5,295 |
| African / African-American | 0.00804% | 12,432 |
| Admixed American | 0.00342% | 29,208 |
| East Asian | 0.00223% | 44,896 |
| European (non-Finnish) | 0.00221% | 45,333 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,320 |
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.Ser472=
- Coding
- c.1416G>A
- MANE Select
- NM_001128148
- dbSNP
- rs776990727
- Type
- single nucleotide variant
- Location
- chr3:196062634 (GRCh38)
- Gene constraint
- LOEUF 0.489 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 86.87 · 24 PDB
- Residue 472
- a turn
Similar variants
- TFRC p.Ser472Leu Uncertain significance ★ ⚠ same residue
- 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
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-ser472 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown