AHNAK p.Ser3159=
c.9477C>T · rs149953106 · VCV727100
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.113%, 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 1.2 | GERP 1.5, phastCons 0.67 |
| Overall | ||
| CADD | 4.28 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.113%
African / African-American · 85/74,980 alleles
Filtering AF
0.0939%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0867%
Overall
0.00589%
95/1,614,024 alleles · rare
exomes 41/1,461,892 · genomes 54/152,132 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.113% | 882 |
| East Asian | 0.0111% | 8,974 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,628 |
| Admixed American | 0.00167% | 59,994 |
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.Ser3159=
- Coding
- c.9477C>T
- MANE Select
- NM_001620
- dbSNP
- rs149953106
- Type
- single nucleotide variant
- Location
- chr11:62524940 (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-ser3159 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown