Is ACTB c.802+20del pathogenic?

ACTB c.802+20del is classified Likely benign in ACTB (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-30). Very rare (popmax 0.000424%, nfe); Associated with Baraitser-Winter syndrome 1.

What condition is associated with ACTB c.802+20del?

ACTB c.802+20del is associated with Baraitser-Winter syndrome 1 (ClinVar).

How common is ACTB c.802+20del in the general population?

ACTB c.802+20del is very rare (popmax 0.000424%, nfe) (gnomAD).

ACTB c.802+20del

VCV4737453

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000424%, nfe)

Conditions

Baraitser-Winter syndrome 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +20	near-intronic (+20 nt from the splice site)
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -2.1	GERP -3.3
Region caveats
Repeat context	seg dup	· reads may not map uniquely · confidence, not pathogenicity

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000424% European (non-Finnish) · 5/1,179,434 alleles

Filtering AF 0.000124% ClinGen BA1/BS1 input FAF95, joint · FAF99 9e-05%

Overall 0.000342% 5/1,461,210 alleles · very rare

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: ACTB
Coding: c.802+20del
MANE Select: NM_001101
Type: Deletion
Location: chr7:5528261 (GRCh38)
Gene constraint: LOEUF 0.193 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 95.31 · 93 PDB

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

Disease context

Baraitser-Winter syndrome 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ACTB p.Leu110fs Pathogenic ★ same condition
ACTB p.Ala181_Leu185del Uncertain significance ★ same condition
ACTB p.Asp222_Phe223del Uncertain significance ★ same condition
ACTB p.Gln225fs Uncertain significance ★ same condition
ACTB p.Gln263fs Uncertain significance ★ same condition
ACTB p.Leu171_Ala174del Uncertain significance ★ same condition
ACTB p.Lys315del Uncertain significance ★ same condition
ACTB p.Met355fs 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/actb-c-802-plus-20del (accessed [today's date]).

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