Is ABCA1 p.Ser824= (c.2472G>A) pathogenic?

ABCA1 p.Ser824= (c.2472G>A) is classified Benign/Likely benign in ABCA1 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-10-16). Rare (popmax 0.67%, sas); Associated with Cardiovascular phenotype.

What condition is associated with ABCA1 p.Ser824= (c.2472G>A)?

ABCA1 p.Ser824= (c.2472G>A) is associated with Cardiovascular phenotype (ClinVar).

How common is ABCA1 p.Ser824= (c.2472G>A) in the general population?

ABCA1 p.Ser824= (c.2472G>A) is rare (popmax 0.67%, sas) (gnomAD).

ABCA1 p.Ser824=

c.2472G>A · rs533413438 · VCV1601505

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.67%, sas)

Conditions

Cardiovascular phenotype

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
Constraint at this position
Conservation	phyloP -15	GERP -4.2
Overall
CADD	0.166	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.67% South Asian · 610/91,078 alleles

Filtering AF 0.626% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.608%

Overall 0.0398% 642/1,614,158 alleles · rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.67%	149
Middle Eastern	0.0495%	2,021
Remaining individualsnot grpmax-eligible	0.0336%	2,977
East Asian	0.00223%	44,880
African / African-American	0.00133%	75,034
European (non-Finnish)	0.000508%	196,671

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: ABCA1
Protein: p.Ser824=
Coding: c.2472G>A
MANE Select: NM_005502
dbSNP: rs533413438
Type: single nucleotide variant
Location: chr9:104825753 (GRCh38)
Gene constraint: LOEUF 0.563 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.50 · 7 PDB
Residue 824: an α-helix

Full ABCA1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ABCA1 p.Ser824Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
ABCA1 c.4175+1G>T Pathogenic/Likely pathogenic ★★ same condition
ABCA1 p.Thr940Met Pathogenic/Likely pathogenic ★★ same condition
ABCA1 c.3787+5C>A Uncertain significance ★★ same condition
ABCA1 p.Ala1855Ser Uncertain significance ★★ ⚠ same condition
ABCA1 p.Ala766Ser Uncertain significance ★★ ⚠ same condition
ABCA1 p.Arg1283Cys Uncertain significance ★★ ⚠ same condition
ABCA1 p.Arg1342Trp Uncertain significance ★★ ⚠ 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/abca1-p-ser824 (accessed [today's date]).

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