Is ABCA9 p.Ile1108= (c.3324C>T) pathogenic?

ABCA9 p.Ile1108= (c.3324C>T) is classified Likely benign in ABCA9 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-01). Rare (popmax 0.534%, nfe).

How common is ABCA9 p.Ile1108= (c.3324C>T) in the general population?

ABCA9 p.Ile1108= (c.3324C>T) is rare (popmax 0.534%, nfe) (gnomAD).

ABCA9 p.Ile1108=

c.3324C>T · rs150518027 · VCV2648159

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.534%, nfe)

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
Pangolin	Δ0.24	loss · gain 0.00 · not in the SpliceAI release · independent
Constraint at this position
Conservation	phyloP -0.6	GERP -2.2
Overall
CADD	1.651	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.534% European (non-Finnish) · 6,150/1,151,332 alleles

Filtering AF 0.523% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.518%

Overall 0.43% 6,796/1,578,818 alleles · rare

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	1.32%	76
European (non-Finnish)grpmax	0.534%	187
Remaining individualsnot grpmax-eligible	0.415%	241
Admixed American	0.323%	310
Middle Eastern	0.151%	664
Ashkenazi Jewishnot grpmax-eligible	0.13%	769
African / African-American	0.0744%	1,345
South Asian	0.0698%	1,432
Finnishnot grpmax-eligible	0.0391%	2,557
East Asian	0.00224%	44,626

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: ABCA9
Protein: p.Ile1108=
Coding: c.3324C>T
MANE Select: NM_080283
dbSNP: rs150518027
Type: single nucleotide variant
Location: chr17:69007870 (GRCh38)
Gene constraint: LOEUF 1.006 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.22

Full ABCA9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABCA9 p.Tyr1123= Likely benign ★★ same type
ABCA9 p.Ala1071Val Uncertain significance ★ ⚠ same type
ABCA9 p.Ala1153Thr Uncertain significance ★ ⚠ same type
ABCA9 p.Ala1196Thr Uncertain significance ★ ⚠ same type
ABCA9 p.Ala125Thr Uncertain significance ★ ⚠ same type
ABCA9 p.Ala1285Thr Uncertain significance ★ ⚠ same type
ABCA9 p.Ala1407Val Uncertain significance ★ ⚠ same type
ABCA9 p.Ala1492Pro 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/abca9-p-ile1108 (accessed [today's date]).

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