TSFM p.Arg39=
c.117T>A · rs147609698 · VCV378795
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.333%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.01 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 1.4 | GERP -4.6, phastCons 0.013 |
| Overall | ||
| CADD | 5.611 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.333%
African / African-American · 250/75,040 alleles
Filtering AF
0.299%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.286%
Overall
0.0182%
294/1,613,476 alleles · rare
exomes 158/1,461,172 · genomes 136/152,304 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.333% | 300 |
| Middle Eastern | 0.0825% | 1,212 |
| Remaining individualsnot grpmax-eligible | 0.0416% | 2,403 |
| Admixed American | 0.0167% | 6,002 |
| South Asian | 0.00329% | 30,361 |
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
- TSFM
- Protein
- p.Arg39=
- Coding
- c.117T>A
- MANE Select
- NM_005726
- dbSNP
- rs147609698
- Type
- single nucleotide variant
- Location
- chr12:57783169 (GRCh38)
- Gene constraint
- LOEUF 1.197 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.87 · 1 PDB
Similar variants
- TSFM p.Arg39Leu Uncertain significance ★★ ⚠ same residue
- TSFM p.Arg39fs Likely pathogenic ★ same residue
- TSFM c.231+1G>A Likely pathogenic ★★ same type
- TSFM c.232-2A>G Likely pathogenic ★★ same type
- TSFM c.484-1G>A Likely pathogenic ★★ same type
- TSFM c.484-1G>T Likely pathogenic ★★ same type
- TSFM c.57+1G>A Likely pathogenic ★★ same type
- TSFM c.571+1G>C Pathogenic/Likely pathogenic ★★ 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/tsfm-p-arg39 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown