Is ARMS2 p.Pro83fs (c.246_247del) pathogenic?

ARMS2 p.Pro83fs (c.246247del) is classified Likely benign in ARMS2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2022-09-01). Rare (popmax 0.572%, afr).

How common is ARMS2 p.Pro83fs (c.246_247del) in the general population?

ARMS2 p.Pro83fs (c.246_247del) is rare (popmax 0.572%, afr) (gnomAD).

ARMS2 p.Pro83fs

c.246_247del · rs532010317 · VCV723528

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

rare (popmax 0.572%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function; NMD-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -3	GERP -0.69
Overall
CADD	17.78	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.572% African / African-American · 429/75,028 alleles

Filtering AF 0.527% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.51%

Overall 0.029% 468/1,613,652 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.572%	175
Remaining individualsnot grpmax-eligible	0.0288%	3,471
Admixed American	0.0167%	6,000
Middle Eastern	0.0165%	6,062
South Asian	0.00879%	11,382
European (non-Finnish)	0.00017%	589,828

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: ARMS2
Protein: p.Pro83fs
Coding: c.246_247del
dbSNP: rs532010317
Type: Microsatellite
Location: chr10:122454969 (GRCh38)

Full ARMS2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/arms2-p-pro83fs (accessed [today's date]).

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