TSFM p.Arg5=
c.13C>A · rs1955528884 · VCV1672834
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00228%, 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 -0.18 | GERP -2.8 |
| Overall | ||
| CADD | 7.414 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00228%
South Asian · 2/87,678 alleles
Filtering AF
0.000379%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000142%
Overall
0.000188%
3/1,592,762 alleles · very rare
exomes 3/1,440,456 · genomes 0/152,306 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00228% | 43,839 |
| European (non-Finnish) | 8.54e-05% | 1,170,513 |
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.Arg5=
- Coding
- c.13C>A
- MANE Select
- NM_005726
- dbSNP
- rs1955528884
- Type
- single nucleotide variant
- Location
- chr12:57782814 (GRCh38)
- Gene constraint
- LOEUF 1.197 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.87 · 1 PDB
Similar variants
- 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
- TSFM p.Arg201Ter Pathogenic/Likely pathogenic ★★ same type
- TSFM p.Arg312Trp 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-arg5 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown