ANK3 p.Phe1460=
c.4380C>T · rs75052415 · VCV1166909
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 11%, 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. | ||
| REVEL | 0.267 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.28 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 2.8 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 12.69 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
11%
East Asian · 4,925/44,692 alleles
Filtering AF
10.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 10.7%
Overall
0.462%
7,417/1,604,872 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 11% | 9 |
| South Asian | 1.7% | 59 |
| Remaining individualsnot grpmax-eligible | 0.54% | 185 |
| Ashkenazi Jewishnot grpmax-eligible | 0.166% | 601 |
| Amishnot grpmax-eligible | 0.11% | 912 |
| Middle Eastern | 0.0993% | 1,007 |
| Finnishnot grpmax-eligible | 0.0536% | 1,866 |
| Admixed American | 0.0481% | 2,077 |
| European (non-Finnish) | 0.0449% | 2,226 |
| African / African-American | 0.0121% | 8,255 |
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
- ANK3
- Protein
- p.Phe1460=
- Coding
- c.4380C>T
- MANE Select
- NM_020987
- dbSNP
- rs75052415
- Type
- single nucleotide variant
- Location
- chr10:60080589 (GRCh38)
- Gene constraint
- LOEUF 0.16 · pLI 1.00 (gnomAD)
Similar variants
- ANK3 c.2382+6C>T Uncertain significance ★★ same type
- ANK3 p.Ala1461Thr Uncertain significance ★★ ⚠ same type
- ANK3 p.Ala1534Val Uncertain significance ★★ same type
- ANK3 p.Ala1630Val Uncertain significance ★★ ⚠ same type
- ANK3 p.Ala169Thr Uncertain significance ★★ same type
- ANK3 p.Ala2023Thr Uncertain significance ★★ ⚠ same type
- ANK3 p.Ala218Thr Uncertain significance ★★ same type
- ANK3 p.Ala2223Thr 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/ank3-p-phe1460 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown