Is AHNAK2 p.Val899Leu (c.2695G>T) pathogenic?

AHNAK2 p.Val899Leu (c.2695G>T) is classified Benign in AHNAK2 (ClinVar, Single submitter, 2 submitters). AlphaMissense: likely benign (0.1747); Rare (popmax 0.359%, afr).

How common is AHNAK2 p.Val899Leu (c.2695G>T) in the general population?

AHNAK2 p.Val899Leu (c.2695G>T) is rare (popmax 0.359%, afr) (gnomAD).

What do computational predictors say about AHNAK2 p.Val899Leu (c.2695G>T)?

AlphaMissense predicts likely benign (score 0.1747) — an in-silico prediction, not a clinical call.

AHNAK2 p.Val899Leu

c.2695G>T · rs199974920 · VCV208975

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1747 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.359%, afr)

Missense predictors

0/2 damaging

AlphaMissense, REVEL · SaProt no call

Computational evidence

Protein change
AlphaMissense	0.1747	likely benign
REVEL	0.06	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 -20	GERP -1.9
Regional constraint	o/e 1.23	unconstrained · MANE · 32 kb · p 4.7e-50 · regional, not allelic
Overall
CADD	0.003	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 0.359% African / African-American · 267/74,372 alleles

Filtering AF 0.324% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.31%

Overall 0.0178% 287/1,612,678 alleles · rare exomes 145/1,461,346 · genomes 142/151,332 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.359%	279
Middle Eastern	0.0661%	1,513
Remaining individualsnot grpmax-eligible	0.0128%	7,806
Admixed American	0.01%	9,993
European (non-Finnish)	0.00017%	589,803

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.Val899Leu
Coding: c.2695G>T
MANE Select: NM_138420
dbSNP: rs199974920
Type: single nucleotide variant
Location: chr14:104952756 (GRCh38)
Gene constraint: LOEUF 0.917 · pLI <0.01 (gnomAD)

Full AHNAK2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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-val899leu (accessed [today's date]).

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