ANK3 p.Leu3420=
c.10258C>T · rs146174990 · VCV726789
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.86%, afr)
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 7.6 | GERP 5.3, phastCons 1 |
| Overall | ||
| CADD | 6.764 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.86%
African / African-American · 1,392/75,028 alleles
Filtering AF
1.77%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.74%
Overall
0.107%
1,724/1,614,124 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.86% | 54 |
| Remaining individualsnot grpmax-eligible | 0.104% | 962 |
| Admixed American | 0.0967% | 1,034 |
| Middle Eastern | 0.0495% | 2,020 |
| European (non-Finnish) | 0.0169% | 5,930 |
| Finnishnot grpmax-eligible | 0.00469% | 21,345 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,608 |
| South Asian | 0.00329% | 30,361 |
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.Leu3420=
- Coding
- c.10258C>T
- MANE Select
- NM_020987
- dbSNP
- rs146174990
- Type
- single nucleotide variant
- Location
- chr10:60070623 (GRCh38)
- Gene constraint
- LOEUF 0.16 · pLI 1.00 (gnomAD)
- Residue 3420
- the 'disordered' region
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-leu3420 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown