AHR p.Arg554=
c.1662A>G · rs139289489 · VCV1529916
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00769%, 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 0.12 | GERP -3.8 |
| Overall | ||
| CADD | 3.343 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00769%
South Asian · 7/91,082 alleles
Filtering AF
0.00359%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00255%
Overall
0.000547%
8/1,461,814 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00769% | 13,012 |
| European (non-Finnish) | 8.47e-05% | 1,180,011 |
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
- AHR
- Protein
- p.Arg554=
- Coding
- c.1662A>G
- MANE Select
- NM_001621
- dbSNP
- rs139289489
- Type
- single nucleotide variant
- Location
- chr7:17339487 (GRCh38)
- Gene constraint
- LOEUF 0.606 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 56.88 · 3 PDB
- Residue 554
- a UniProt-annotated variant site (in)
Similar variants
- AHR p.Arg554Lys Benign ★★ same residue
- AHR p.Ala313Thr Uncertain significance ★★ ⚠ same type
- AHR p.Ala459Ser Uncertain significance ★★ ⚠ same type
- AHR p.Arg352Trp Uncertain significance ★★ ⚠ same type
- AHR p.Asn179His Uncertain significance ★★ ⚠ same type
- AHR p.Asn238Ser Uncertain significance ★★ ⚠ same type
- AHR p.Asn789Ser Uncertain significance ★★ ⚠ same type
- AHR p.Asp841Asn 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/ahr-p-arg554 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown