AHNAK2 p.Pro3151=
c.9453G>A · rs202104959 · VCV2644688
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0758%, 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 -0.61 |
| Overall | ||
| CADD | 2.345 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0758%
European (non-Finnish) · 719/949,030 alleles
Filtering AF
0.0711%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0693%
Overall
0.0585%
776/1,327,390 alleles · ultra-rare
exomes 767/1,209,648 · genomes 9/117,742 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0758% | 1,320 |
| Remaining individualsnot grpmax-eligible | 0.0309% | 3,241 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0242% | 4,139 |
| Middle Eastern | 0.023% | 4,356 |
| South Asian | 0.0195% | 5,134 |
| African / African-American | 0.0129% | 7,757 |
| Admixed American | 0.011% | 9,064 |
| Finnishnot grpmax-eligible | 0.00723% | 13,837 |
| East Asian | 0.00226% | 44,206 |
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.Pro3151=
- Coding
- c.9453G>A
- MANE Select
- NM_138420
- dbSNP
- rs202104959
- Type
- single nucleotide variant
- Location
- chr14:104945998 (GRCh38)
- Gene constraint
- LOEUF 0.917 · pLI <0.01 (gnomAD)
Similar variants
- AHNAK2 p.Pro3151Leu 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
- AHNAK2 p.Ala1323Thr 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-pro3151 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown