ABCD4 c.38+276G>A
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 82.7%, eas) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type. | ||
| Splicing | ||
| Splice region | donor +276 | deep intronic (+276 nt into the intron) |
|---|---|---|
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.23 · evaluated, not missing |
| Constraint at this position | ||
| Non-coding constraint | Z -0.23 | 1 kb window · o/e 1.02 · regional · uncalibrated |
| Overall | ||
| CADD | 4.109 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
82.7%
East Asian · 4,254/5,146 alleles
Filtering AF
80.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 79.7%
Overall
57.9%
87,636/151,400 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 82.7% | 1 |
| Middle Eastern | 76.9% | 1 |
| African / African-American | 75.4% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 63.3% | 2 |
| Remaining individualsnot grpmax-eligible | 62.5% | 2 |
| South Asian | 58% | 2 |
| Admixed American | 55.8% | 2 |
| Amishnot grpmax-eligible | 50.1% | 2 |
| European (non-Finnish) | 48.7% | 2 |
| Finnishnot grpmax-eligible | 37.4% | 3 |
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
- ABCD4
- Coding
- c.38+276G>A
- MANE Select
- NM_005050
- dbSNP
- rs4148073
- Type
- single nucleotide variant
- Location
- chr14:74302599 (GRCh38)
- Gene constraint
- LOEUF 0.772 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.18 · 4 PDB
Similar variants
- ABCD4 c.542+1G>T Pathogenic ★★ same type
- ABCD4 p.Arg432Gln Likely pathogenic ★★ same type
- ABCD4 p.Asn141Lys Pathogenic/Likely pathogenic ★★ same type
- ABCD4 p.Gln530Ter Pathogenic/Likely pathogenic ★★ same type
- ABCD4 p.Tyr176Ter Pathogenic/Likely pathogenic ★★ same type
- ABCD4 c.1028+5G>A Uncertain significance ★★ same type
- ABCD4 c.425+6C>T Uncertain significance ★★ same type
- ABCD4 c.719+6T>C 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/abcd4-c-38-plus-276g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown