AHNAK2 p.Asp3465=
c.10395T>C · rs529172064 · VCV2644671
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0333%, 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 0.69 | GERP -1.1, phastCons 0.021 |
| Overall | ||
| CADD | 0.124 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0333%
Middle Eastern · 2/6,012 alleles
Filtering AF
0.0173%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0137%
Overall
0.00454%
73/1,606,984 alleles · ultra-rare
exomes 47/1,461,100 · genomes 26/145,884 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0333% | 3,006 |
| East Asian | 0.0293% | 3,408 |
| African / African-American | 0.0219% | 4,558 |
| Admixed American | 0.00672% | 14,870 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00339% | 29,468 |
| South Asian | 0.00331% | 30,248 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,174 |
| European (non-Finnish) | 0.00272% | 36,784 |
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.Asp3465=
- Coding
- c.10395T>C
- MANE Select
- NM_138420
- dbSNP
- rs529172064
- Type
- single nucleotide variant
- Location
- chr14:104945056 (GRCh38)
- Gene constraint
- LOEUF 0.917 · pLI <0.01 (gnomAD)
Similar variants
- AHNAK2 p.Asp3465Glu Uncertain significance ★ ⚠ same residue
- AHNAK2 p.Asp3465fs Uncertain significance ★ same residue
- 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
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-asp3465 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown