ARNT2 p.Thr605=
c.1815C>G · rs79914316 · VCV1166612
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Common
common (popmax 14.6%, eas) — too common for a highly-penetrant pathogenic allele
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 0.66 | GERP -1.5, phastCons 0.27 |
| Overall | ||
| CADD | 7.531 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
14.6%
East Asian · 6,545/44,870 alleles
Filtering AF
14.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 14.2%
Overall
2.12%
34,249/1,614,118 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 14.6% | 7 |
| African / African-American | 12.7% | 8 |
| Finnishnot grpmax-eligible | 8.58% | 12 |
| South Asian | 6.74% | 15 |
| Remaining individualsnot grpmax-eligible | 2.56% | 39 |
| Admixed American | 2.44% | 41 |
| Ashkenazi Jewishnot grpmax-eligible | 2.04% | 49 |
| Middle Eastern | 1.73% | 58 |
| European (non-Finnish) | 0.237% | 422 |
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
- ARNT2
- Protein
- p.Thr605=
- Coding
- c.1815C>G
- MANE Select
- NM_014862
- dbSNP
- rs79914316
- Type
- single nucleotide variant
- Location
- chr15:80581301 (GRCh38)
- Gene constraint
- LOEUF 0.498 · pLI 0.94 (gnomAD)
- Structure
- AlphaFold pLDDT 59.49
- Residue 605
- the 'disordered' region
Similar variants
- ARNT2 p.Arg159Ter Pathogenic/Likely pathogenic ★★ same type
- ARNT2 p.Ala483Val Uncertain significance ★★ ⚠ same type
- ARNT2 p.Arg262Lys Uncertain significance ★★ ⚠ same type
- ARNT2 p.Asp705Tyr Uncertain significance ★★ ⚠ same type
- ARNT2 p.Gln520Arg Uncertain significance ★★ ⚠ same type
- ARNT2 p.Gly472Ser Uncertain significance ★★ ⚠ same type
- ARNT2 p.Gly546Arg Uncertain significance ★★ ⚠ same type
- ARNT2 p.Ile347Phe 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/arnt2-p-thr605 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown