AHNAK p.Pro4289=
c.12867A>T · rs1321366614 · VCV2641863
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0337%, mid)
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 -20 | GERP -3.4 |
| Overall | ||
| CADD | 0.085 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0337%
Middle Eastern · 2/5,938 alleles
Filtering AF
0.00905%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00656%
Overall
0.00226%
36/1,594,420 alleles · ultra-rare
exomes 0/1,458,128 · genomes 36/136,292 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0337% | 2,969 |
| East Asian | 0.0183% | 5,458 |
| African / African-American | 0.0143% | 6,982 |
| Admixed American | 0.00345% | 28,966 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00343% | 29,182 |
| Finnishnot grpmax-eligible | 0.00317% | 31,592 |
| South Asian | 0.00111% | 89,886 |
| European (non-Finnish) | 0.000853% | 117,203 |
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.Pro4289=
- Coding
- c.12867A>T
- MANE Select
- NM_001620
- dbSNP
- rs1321366614
- Type
- single nucleotide variant
- Location
- chr11:62521550 (GRCh38)
- Gene constraint
- LOEUF 0.793 · pLI <0.01 (gnomAD)
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-pro4289 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown