Is ARMC3 p.Asn98= (c.294T>C) pathogenic?

ARMC3 p.Asn98= (c.294T>C) is classified Likely benign in ARMC3 (ClinVar, No assertion criteria, 1 submitter). Very rare (popmax 8.54e-05%, nfe); Associated with EBV-positive nodal T- and NK-cell lymphoma.

What condition is associated with ARMC3 p.Asn98= (c.294T>C)?

ARMC3 p.Asn98= (c.294T>C) is associated with EBV-positive nodal T- and NK-cell lymphoma (ClinVar).

How common is ARMC3 p.Asn98= (c.294T>C) in the general population?

ARMC3 p.Asn98= (c.294T>C) is very rare (popmax 8.54e-05%, nfe) (gnomAD).

ARMC3 p.Asn98=

c.294T>C · rs1471803837 · VCV2681414

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.54e-05%, nfe)

Conditions

EBV-positive nodal T- and NK-cell lymphoma

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · T>A here scores Δ0.33 · evaluated, not missing
Constraint at this position
Conservation	phyloP 0.69	GERP 0.37, phastCons 1
Overall
CADD	9.057	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.54e-05% European (non-Finnish) · 1/1,170,444 alleles

Overall 6.89e-05% 1/1,451,248 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: ARMC3
Protein: p.Asn98=
Coding: c.294T>C
MANE Select: NM_173081
dbSNP: rs1471803837
Type: single nucleotide variant
Location: chr10:22959071 (GRCh38)
Gene constraint: LOEUF 0.91 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.81

Full ARMC3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

EBV-positive nodal T- and NK-cell lymphoma

Similar variants

ARMC3 c.916+1G>A Uncertain significance ★ same condition
ARMC3 p.Met441Ile Uncertain significance ★★ ⚠ same type
ARMC3 p.Ala115Asp Uncertain significance ★ ⚠ same type
ARMC3 p.Ala118Thr Uncertain significance ★ ⚠ same type
ARMC3 p.Ala138Ser Uncertain significance ★ ⚠ same type
ARMC3 p.Ala192Ser Uncertain significance ★ ⚠ same type
ARMC3 p.Ala211Val Uncertain significance ★ ⚠ same type
ARMC3 p.Ala335Thr 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/armc3-p-asn98 (accessed [today's date]).

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