Is ACVR2B p.Ala3= (c.9G>A) pathogenic?

ACVR2B p.Ala3= (c.9G>A) is classified Likely benign in ACVR2B (ClinVar, Single submitter, 1 submitter; last evaluated 2022-02-21). Very rare (popmax 0.00677%, amr); Associated with heterotaxy, visceral, 4, autosomal.

What condition is associated with ACVR2B p.Ala3= (c.9G>A)?

ACVR2B p.Ala3= (c.9G>A) is associated with heterotaxy, visceral, 4, autosomal (ClinVar).

How common is ACVR2B p.Ala3= (c.9G>A) in the general population?

ACVR2B p.Ala3= (c.9G>A) is very rare (popmax 0.00677%, amr) (gnomAD).

ACVR2B p.Ala3=

c.9G>A · rs1246364065 · VCV2151463

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00677%, amr)

Conditions

heterotaxy, visceral, 4, autosomal

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 4.3	GERP -0.15, phastCons 1
Overall
CADD	15.82	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00677% Admixed American · 2/29,532 alleles

Filtering AF 0.00112% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000419%

Overall 0.000231% 3/1,298,526 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00677%	14,766
European (non-Finnish)	9.77e-05%	1,023,326

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: ACVR2B
Protein: p.Ala3=
Coding: c.9G>A
dbSNP: rs1246364065
Type: single nucleotide variant
Location: chr3:38454331 (GRCh38)

Full ACVR2B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

heterotaxy, visceral, 4, autosomal — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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/acvr2b-p-ala3 (accessed [today's date]).

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