Is ARMS2 p.Ala13= (c.39G>A) pathogenic?

ARMS2 p.Ala13= (c.39G>A) is classified Uncertain significance in ARMS2 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-13). Rare (popmax 0.103%, amr); Associated with age related macular degeneration 8.

What condition is associated with ARMS2 p.Ala13= (c.39G>A)?

ARMS2 p.Ala13= (c.39G>A) is associated with age related macular degeneration 8 (ClinVar).

How common is ARMS2 p.Ala13= (c.39G>A) in the general population?

ARMS2 p.Ala13= (c.39G>A) is rare (popmax 0.103%, amr) (gnomAD).

ARMS2 p.Ala13=

c.39G>A · rs200123144 · VCV878186

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.103%, amr)

Conditions

age related macular degeneration 8

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 0.001	GERP -0.49
Overall
CADD	5.795	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.103% Admixed American · 62/59,996 alleles

Filtering AF 0.0827% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0752%

Overall 0.0118% 190/1,613,850 alleles · rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.103%	968
Middle Eastern	0.0822%	1,216
Remaining individualsnot grpmax-eligible	0.0336%	2,975
European (non-Finnish)	0.00788%	12,687
African / African-American	0.00667%	14,983
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,606
South Asian	0.00329%	30,359

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.Ala13=
Coding: c.39G>A
dbSNP: rs200123144
Type: single nucleotide variant
Location: chr10:122454766 (GRCh38)

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

Disease context

age related macular degeneration 8 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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-ala13 (accessed [today's date]).

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