TMPRSS2 p.Arg489=
c.1467G>A · rs142750000 · VCV425275
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.648%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not looked up on this page · why |
|---|---|---|
| Pangolin | Δ0.58 | loss · gain 0.01 · independent |
| Constraint at this position | ||
| Conservation | phyloP 7.3 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 20.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.648%
European (non-Finnish) · 7,642/1,179,940 alleles
Filtering AF
0.635%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.63%
Overall
0.502%
8,096/1,614,000 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.648% | 154 |
| Remaining individualsnot grpmax-eligible | 0.37% | 271 |
| African / African-American | 0.121% | 824 |
| Admixed American | 0.115% | 870 |
| South Asian | 0.0417% | 2,396 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0304% | 3,288 |
| Finnishnot grpmax-eligible | 0.0234% | 4,269 |
| Middle Eastern | 0.0165% | 6,062 |
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
- TMPRSS2
- Protein
- p.Arg489=
- Coding
- c.1467G>A
- MANE Select
- NM_002462 · reported on NM_005656
- dbSNP
- rs142750000
- Type
- single nucleotide variant
- Location
- chr21:41467734 (GRCh38)
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/tmprss2-p-arg489 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown