AHNAK p.Pro4625=
c.13875C>T · rs12793602 · VCV773246
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.672%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -3.6 |
| Overall | ||
| CADD | 0.491 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.672%
European (non-Finnish) · 7,933/1,179,804 alleles
Filtering AF
0.66%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.655%
Overall
0.529%
8,533/1,613,262 alleles · rare
exomes 8,023/1,461,890 · genomes 510/151,372 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.672% | 149 |
| Remaining individualsnot grpmax-eligible | 0.378% | 265 |
| African / African-American | 0.257% | 389 |
| Middle Eastern | 0.132% | 755 |
| Finnishnot grpmax-eligible | 0.12% | 831 |
| Admixed American | 0.117% | 856 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0169% | 5,919 |
| South Asian | 0.0121% | 8,275 |
| East Asian | 0.00223% | 44,804 |
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
- AHNAK
- Protein
- p.Pro4625=
- Coding
- c.13875C>T
- MANE Select
- NM_001620
- dbSNP
- rs12793602
- Type
- single nucleotide variant
- Location
- chr11:62520542 (GRCh38)
- Gene constraint
- LOEUF 0.793 · pLI <0.01 (gnomAD)
- Residue 4625
- the 'disordered' region
Similar variants
- AHNAK p.Asn3289His Uncertain significance ★★ ⚠ same type
- AHNAK p.Gly365Val Uncertain significance ★★ ⚠ same type
- AHNAK p.Ala3588= Benign/Likely benign ★★ same type
- AHNAK p.Arg1063Lys Benign ★★ same type
- AHNAK p.Arg1272Pro Benign ★★ same type
- AHNAK p.Asn3587Ser Benign ★★ same type
- AHNAK p.Asp1493= Benign ★★ same type
- AHNAK p.Asp2459= Benign ★★ 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/ahnak-p-pro4625 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown