AHNAK p.Asp2459=
c.7377T>C · rs75858820 · VCV783606
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.6%, 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 -4.2 | GERP -3.6 |
| Overall | ||
| CADD | 0.258 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.6%
African / African-American · 2,700/75,000 alleles
Filtering AF
3.49%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.44%
Overall
0.189%
3,052/1,614,026 alleles · low-frequency
exomes 1,547/1,461,808 · genomes 1,505/152,218 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.6% | 28 |
| Remaining individualsnot grpmax-eligible | 0.296% | 338 |
| Middle Eastern | 0.231% | 433 |
| Admixed American | 0.175% | 572 |
| South Asian | 0.00988% | 10,118 |
| European (non-Finnish) | 0.00322% | 31,052 |
| East Asian | 0.00223% | 44,874 |
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.Asp2459=
- Coding
- c.7377T>C
- MANE Select
- NM_001620
- dbSNP
- rs75858820
- Type
- single nucleotide variant
- Location
- chr11:62527040 (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.Asp2803= 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-asp2459 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown