Is ACKR1 p.Val32Met (c.94G>A) pathogenic?

ACKR1 p.Val32Met (c.94G>A) is classified Uncertain significance in ACKR1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-01). AlphaMissense: likely benign (0.1224); Absent from gnomAD v4.1.

How common is ACKR1 p.Val32Met (c.94G>A) in the general population?

ACKR1 p.Val32Met (c.94G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ACKR1 p.Val32Met (c.94G>A)?

AlphaMissense predicts likely benign (score 0.1224) — an in-silico prediction, not a clinical call.

ACKR1 p.Val32Met

c.94G>A · VCV3998512

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1224 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1224	likely benign
REVEL	0.028	moderately benign-leaning
SaProt	LLR -7.58	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Pangolin	Δ0.25	gain · loss 0.00 · not in the SpliceAI release · independent
Constraint at this position
Conservation	phyloP 0.005	GERP -3.3
Regional constraint	o/e 1.11	unconstrained · MANE · 1,487 bp · p 0.031 · regional, not allelic
Overall
CADD	10.91	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: ACKR1
Protein: p.Val32Met
Coding: c.94G>A
MANE Select: NM_002036
Type: single nucleotide variant
Location: chr1:159205533 (GRCh38)
Gene constraint: LOEUF 1.841 · pLI 0.02 (gnomAD)
Structure: AlphaFold pLDDT 78.25 · 6 PDB

Full ACKR1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ACKR1 p.Arg89Cys Likely benign ★★ same type
ACKR1 p.Gly238= Benign ★★ same type
ACKR1 p.Gly42Asp Benign ★★ same type
ACKR1 p.Ala144Pro Uncertain significance ★ ⚠ same type
ACKR1 p.Ala49Val Uncertain significance ★ ⚠ same type
ACKR1 p.Asn244Ser Uncertain significance ★ ⚠ same type
ACKR1 p.Asp283Gly Uncertain significance ★ ⚠ same type
ACKR1 p.Cys51Trp Uncertain significance ★ ⚠ 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/ackr1-p-val32met (accessed [today's date]).

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