Is ARMC5 p.Ala702= (c.2106G>A) pathogenic?

ARMC5 p.Ala702= (c.2106G>A) is classified Likely benign in ARMC5 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-03-19). Very rare (popmax 0.00934%, afr); Associated with ARMC5-related disorder.

What condition is associated with ARMC5 p.Ala702= (c.2106G>A)?

ARMC5 p.Ala702= (c.2106G>A) is associated with ARMC5-related disorder (ClinVar).

How common is ARMC5 p.Ala702= (c.2106G>A) in the general population?

ARMC5 p.Ala702= (c.2106G>A) is very rare (popmax 0.00934%, afr) (gnomAD).

ARMC5 p.Ala702=

c.2106G>A · rs777189617 · VCV3047624

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00934%, afr)

Conditions

ARMC5-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.57	acceptor gain · deltas
Constraint at this position
Conservation	phyloP -4.5	GERP -3.1
Overall
CADD	13.86	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00934% African / African-American · 7/74,924 alleles

Filtering AF 0.00437% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00312%

Overall 0.00167% 27/1,612,340 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00934%	10,703
South Asian	0.00878%	11,386
Remaining individualsnot grpmax-eligible	0.0048%	20,819
East Asian	0.00223%	44,874
Admixed American	0.00167%	60,002
European (non-Finnish)	0.000593%	168,556

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: ARMC5
Protein: p.Ala702=
Coding: c.2106G>A
MANE Select: NM_001105247
dbSNP: rs777189617
Type: single nucleotide variant
Location: chr16:31466187 (GRCh38)
Gene constraint: LOEUF 0.772 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.27
Residue 702: a UniProt-annotated variant site (in aimah2; uncertain significance); a UniProt-annotated variant site (in aimah2); a UniProt-annotated variant site (in aimah2; likely pathogenic)

Full ARMC5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ARMC5-related disorder

Similar variants

ARMC5 p.Ala702Glu Likely pathogenic ★ ⚠ same residue
ARMC5 p.Arg173Ter Pathogenic ★★ same condition
ARMC5 p.Arg690Gln Uncertain significance ★★ ⚠ same condition
ARMC5 p.Pro606Leu Uncertain significance ★★ ⚠ same condition
ARMC5 p.Arg267Ter Pathogenic ★ same condition
ARMC5 p.Arg315Pro Likely pathogenic ★ same condition
ARMC5 p.Gln759Ter Likely pathogenic ★ same condition
ARMC5 p.Ser107Ter Likely pathogenic ★ 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/armc5-p-ala702 (accessed [today's date]).

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