ANKS1A p.Pro83=
c.249C>G · rs147758055 · VCV3067220
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.363%, 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 -1.4 | GERP -2.5 |
| Overall | ||
| CADD | 6.111 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.363%
European (non-Finnish) · 4,280/1,179,982 alleles
Filtering AF
0.354%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.35%
Overall
0.289%
4,672/1,613,992 alleles · rare
exomes 4,403/1,461,858 · genomes 269/152,134 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.363% | 276 |
| Remaining individualsnot grpmax-eligible | 0.259% | 386 |
| Finnishnot grpmax-eligible | 0.153% | 653 |
| Admixed American | 0.0883% | 1,132 |
| African / African-American | 0.068% | 1,470 |
| South Asian | 0.0296% | 3,373 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
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
- ANKS1A
- Protein
- p.Pro83=
- Coding
- c.249C>G
- MANE Select
- NM_015245
- dbSNP
- rs147758055
- Type
- single nucleotide variant
- Location
- chr6:34967290 (GRCh38)
- Gene constraint
- LOEUF 0.549 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.78 · 3 PDB
Similar variants
- ANKS1A p.Pro1089= Likely benign ★★ same type
- ANKS1A p.Ala1061Val Uncertain significance ★ ⚠ same type
- ANKS1A p.Ala1076Thr Uncertain significance ★ ⚠ same type
- ANKS1A p.Ala1101Thr Uncertain significance ★ ⚠ same type
- ANKS1A p.Ala268Thr Uncertain significance ★ ⚠ same type
- ANKS1A p.Ala488Val Uncertain significance ★ ⚠ same type
- ANKS1A p.Ala554Asp Uncertain significance ★ ⚠ same type
- ANKS1A p.Ala603Val 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/anks1a-p-pro83 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown