Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.5%, nfe)
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 -0.14 | GERP -6.9 |
| Overall | ||
| CADD | 0.832 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.5%
European (non-Finnish) · 41,245/1,179,994 alleles
Filtering AF
3.47%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.46%
Overall
2.88%
46,563/1,614,060 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 3.5% | 29 |
| Remaining individualsnot grpmax-eligible | 2.41% | 42 |
| Finnishnot grpmax-eligible | 2.24% | 45 |
| Admixed American | 1.66% | 60 |
| Ashkenazi Jewishnot grpmax-eligible | 0.851% | 117 |
| South Asian | 0.665% | 150 |
| African / African-American | 0.529% | 189 |
| Middle Eastern | 0.413% | 242 |
| East Asian | 0.223% | 449 |
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.Ser3895=
- Coding
- c.11685C>T
- MANE Select
- NM_020987
- dbSNP
- rs7923682
- Type
- single nucleotide variant
- Location
- chr10:60069196 (GRCh38)
- Gene constraint
- LOEUF 0.16 · pLI 1.00 (gnomAD)
- Residue 3895
- the 'disordered' region
Similar variants
- ANK3 p.Ser3895Pro Uncertain significance ★★ ⚠ same residue
- 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
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-ser3895 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown