AHNAK2 p.Asp3112=
c.9336T>C · rs759834140 · VCV2644689
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0402%, 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 -20 | GERP -0.77 |
| Overall | ||
| CADD | 0.155 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0402%
European (non-Finnish) · 473/1,177,262 alleles
Filtering AF
0.0371%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.036%
Overall
0.0343%
551/1,607,342 alleles · ultra-rare
exomes 516/1,460,058 · genomes 35/147,284 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0402% | 2,489 |
| Remaining individualsnot grpmax-eligible | 0.0401% | 2,491 |
| Middle Eastern | 0.0332% | 3,013 |
| South Asian | 0.0209% | 4,774 |
| African / African-American | 0.0177% | 5,664 |
| East Asian | 0.0158% | 6,309 |
| Admixed American | 0.0152% | 6,595 |
| Finnishnot grpmax-eligible | 0.00472% | 21,165 |
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
- AHNAK2
- Protein
- p.Asp3112=
- Coding
- c.9336T>C
- MANE Select
- NM_138420
- dbSNP
- rs759834140
- Type
- single nucleotide variant
- Location
- chr14:104946115 (GRCh38)
- Gene constraint
- LOEUF 0.917 · pLI <0.01 (gnomAD)
Similar variants
- AHNAK2 p.Glu3598Lys Uncertain significance ★★ ⚠ same type
- AHNAK2 p.Gly4376Ser Uncertain significance ★★ ⚠ same type
- AHNAK2 p.Lys2479Arg Uncertain significance ★★ ⚠ same type
- AHNAK2 p.Lys3309Asn Uncertain significance ★★ ⚠ same type
- AHNAK2 p.Val1351Met Uncertain significance ★★ ⚠ same type
- AHNAK2 p.Ala1115Val Benign/Likely benign ★★ same type
- AHNAK2 p.Ala1323Thr Likely benign ★★ same type
- AHNAK2 p.Ala1818Thr Benign/Likely 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/ahnak2-p-asp3112 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown