AHNAK p.Pro2499=
c.7497C>T · rs370900359 · VCV2641873
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.02%, eas)
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 -3.2 |
| Overall | ||
| CADD | 0.88 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.02%
East Asian · 9/44,890 alleles
Filtering AF
0.0104%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00779%
Overall
0.0057%
92/1,614,060 alleles · ultra-rare
exomes 81/1,461,884 · genomes 11/152,176 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.02% | 4,988 |
| European (non-Finnish) | 0.00678% | 14,750 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,253 |
| African / African-American | 0.00133% | 74,978 |
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.Pro2499=
- Coding
- c.7497C>T
- MANE Select
- NM_001620
- dbSNP
- rs370900359
- Type
- single nucleotide variant
- Location
- chr11:62526920 (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-pro2499 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown