Is ACVR2B c.*87A>G pathogenic?

ACVR2B c.87A>G is classified Benign in ACVR2B (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-13). Low-frequency (popmax 3.37%, afr); Associated with heterotaxy, visceral, 4, autosomal.

What condition is associated with ACVR2B c.*87A>G?

ACVR2B c.*87A>G is associated with heterotaxy, visceral, 4, autosomal (ClinVar).

How common is ACVR2B c.*87A>G in the general population?

ACVR2B c.*87A>G is low-frequency (popmax 3.37%, afr) (gnomAD).

ACVR2B c.*87A>G

rs78099173 · VCV344923

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 3.37%, afr)

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 assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.2	GERP 1, phastCons 1
Non-coding constraint	Z 4.79	1 kb window · o/e 0.69 · regional · uncalibrated
Overall
CADD	15.02	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 3.37% African / African-American · 2,310/68,546 alleles

Filtering AF 3.26% ClinGen BA1/BS1 input FAF95, joint · FAF99 3.21%

Overall 0.219% 2,781/1,267,462 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	3.37%	30
Middle Eastern	0.338%	296
Admixed American	0.326%	307
Remaining individualsnot grpmax-eligible	0.323%	310
South Asian	0.0135%	7,416
European (non-Finnish)	0.0107%	9,317
Ashkenazi Jewishnot grpmax-eligible	0.0037%	27,018

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
Coding: c.*87A>G
MANE Select: NM_001106
dbSNP: rs78099173
Type: single nucleotide variant
Location: chr3:38483419 (GRCh38)
Gene constraint: LOEUF 0.408 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 84.18 · 9 PDB

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

Similar variants

ACVR2B c.*4984T>C Uncertain significance ★★ same condition
ACVR2B c.*9473T>C Uncertain significance ★★ same condition
ACVR2B p.Arg161Trp Uncertain significance ★★ ⚠ same condition
ACVR2B p.Arg163His Uncertain significance ★★ ⚠ same condition
ACVR2B p.Arg21His Uncertain significance ★★ ⚠ same condition
ACVR2B p.Arg309His Uncertain significance ★★ ⚠ same condition
ACVR2B p.Arg482Gln Uncertain significance ★★ ⚠ same condition
ACVR2B p.Gln246His Uncertain significance ★★ ⚠ same condition

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-c-star-87a-g (accessed [today's date]).

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