Is ARPC1B p.Asn52= (c.156C>T) pathogenic?

ARPC1B p.Asn52= (c.156C>T) is classified Benign/Likely benign in ARPC1B (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-02-04). Common (popmax 61.4%, afr) — too common for a highly-penetrant pathogenic allele.

ARPC1B p.Asn52=

Q: How common is ARPC1B p.Asn52= (c.156C>T) in the general population?

ARPC1B p.Asn52= (c.156C>T) is common (popmax 61.4%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.156C>T · rs4765 · VCV1170234

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Common

common (popmax 61.4%, afr) — too common for a highly-penetrant pathogenic allele

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 -12	GERP -3.8
Overall
CADD	5.045	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 61.4% African / African-American · 45,962/74,856 alleles

Filtering AF 60.9% ClinGen BA1/BS1 input FAF95, joint · FAF99 60.7%

Overall 9.22% 148,657/1,612,940 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	61.4%	2
Middle Eastern	12.5%	8
Admixed American	11%	9
Remaining individualsnot grpmax-eligible	10.6%	9
Finnishnot grpmax-eligible	10.2%	10
South Asian	8.86%	11
Ashkenazi Jewishnot grpmax-eligible	8.55%	12
Amishnot grpmax-eligible	7.24%	14
European (non-Finnish)	6.06%	16
East Asian	0.238%	419

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: ARPC1B
Protein: p.Asn52=
Coding: c.156C>T
MANE Select: NM_005720
dbSNP: rs4765
Type: single nucleotide variant
Location: chr7:99386776 (GRCh38)
Gene constraint: LOEUF 0.876 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.81 · 4 PDB

Full ARPC1B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ARPC1B c.392+2T>C Pathogenic ★★ same type
ARPC1B c.64+2T>A Pathogenic ★★ same type
ARPC1B p.Ala261= Pathogenic ★★ same type
ARPC1B c.1080+4A>C Uncertain significance ★★ same type
ARPC1B c.170-3C>T Uncertain significance ★★ same type
ARPC1B c.501-5G>A Uncertain significance ★★ same type
ARPC1B p.Ala238Val Uncertain significance ★★ ⚠ same type
ARPC1B p.Ala249Val 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/arpc1b-p-asn52 (accessed [today's date]).

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