Is AHNAK p.Ser5807Phe (c.17420C>T) pathogenic?

AHNAK p.Ser5807Phe (c.17420C>T) is classified Benign in AHNAK (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-01-30). AlphaMissense: likely benign (0.1888); Low-frequency (popmax 1.92%, afr).

How common is AHNAK p.Ser5807Phe (c.17420C>T) in the general population?

AHNAK p.Ser5807Phe (c.17420C>T) is low-frequency (popmax 1.92%, afr) (gnomAD).

What do computational predictors say about AHNAK p.Ser5807Phe (c.17420C>T)?

AlphaMissense predicts likely benign (score 0.1888) — an in-silico prediction, not a clinical call.

AHNAK p.Ser5807Phe

c.17420C>T · rs116528762 · VCV783597

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1888 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.92%, afr)

Missense predictors

0/2 damaging

AlphaMissense, REVEL · SaProt no call

Computational evidence

Protein change
AlphaMissense	0.1888	likely benign
REVEL	0.082	moderately benign-leaning
SaProt	—	not scored · why
⇒ AlphaMissense and REVEL both call this tolerated; SaProt makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.3	GERP 1.4, phastCons 0.72
Regional constraint	o/e 1.01	unconstrained · MANE · 19 kb · p 0.28 · regional, not allelic
Overall
CADD	18.72	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.92% African / African-American · 1,439/75,026 alleles

Filtering AF 1.84% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.8%

Overall 0.102% 1,647/1,614,154 alleles · low-frequency exomes 858/1,461,888 · genomes 789/152,266 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.92%	52
Remaining individualsnot grpmax-eligible	0.173%	579
Middle Eastern	0.165%	606
Admixed American	0.085%	1,177
South Asian	0.00659%	15,180
European (non-Finnish)	0.0028%	35,759

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.Ser5807Phe
Coding: c.17420C>T
MANE Select: NM_001620
dbSNP: rs116528762
Type: single nucleotide variant
Location: chr11:62516997 (GRCh38)
Gene constraint: LOEUF 0.793 · pLI <0.01 (gnomAD)
Residue 5807: the 'disordered' region

Full AHNAK gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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-ser5807phe (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown