ABCA2 c.4550+71A>G

Q: Is ABCA2 c.4550+71A>G pathogenic?

ABCA2 c.4550+71A>G is classified Benign in ABCA2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2021-07-14). Common (popmax 81.1%, eas) — too common for a highly-penetrant pathogenic allele; Associated with intellectual developmental disorder with poor growth and with or without seizures or ataxia.

Q: What condition is associated with ABCA2 c.4550+71A>G?

ABCA2 c.4550+71A>G is associated with intellectual developmental disorder with poor growth and with or without seizures or ataxia (ClinVar).

Q: How common is ABCA2 c.4550+71A>G in the general population?

ABCA2 c.4550+71A>G is common (popmax 81.1%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

rs4880188 · VCV1185357

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 81.1%, eas) — too common for a highly-penetrant pathogenic allele

Conditions

intellectual developmental disorder with poor growth and with or without seizures or ataxia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +71	deep intronic (+71 nt into the intron)
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.5	GERP -1.5
Overall
CADD	7.195	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 81.1% East Asian · 33,861/41,728 alleles

Filtering AF 80.4% ClinGen BA1/BS1 input FAF95, joint · FAF99 80.1%

Overall 70.5% 1,062,006/1,505,376 alleles · common

Ancestry group	Frequency	1 in
East Asiangrpmax	81.1%	1
South Asian	76.3%	1
Amishnot grpmax-eligible	71.1%	1
Ashkenazi Jewishnot grpmax-eligible	71%	1
Remaining individualsnot grpmax-eligible	70.9%	1
European (non-Finnish)	70.4%	1
African / African-American	70.1%	1
Middle Eastern	68.3%	1
Finnishnot grpmax-eligible	67.8%	1
Admixed American	57.3%	2

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: ABCA2
Coding: c.4550+71A>G
MANE Select: NM_001606
dbSNP: rs4880188
Type: single nucleotide variant
Location: chr9:137013390 (GRCh38)
Gene constraint: LOEUF 0.436 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 71.46

Full ABCA2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

intellectual developmental disorder with poor growth and with or without seizures or ataxia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ABCA2 p.Gln1370Ter Likely pathogenic ★★ same condition
ABCA2 p.Ala367Thr Uncertain significance ★★ ⚠ same condition
ABCA2 p.Arg114Gln Uncertain significance ★★ ⚠ same condition
ABCA2 p.Arg1160His Uncertain significance ★★ ⚠ same condition
ABCA2 p.Arg1383His Uncertain significance ★★ ⚠ same condition
ABCA2 p.Arg1664Trp Uncertain significance ★★ ⚠ same condition
ABCA2 p.Arg954His Uncertain significance ★★ ⚠ same condition
ABCA2 p.Asn1755Lys 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/abca2-c-4550-plus-71a-g (accessed [today's date]).

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