ABCD4 c.38+276del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.67%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +276 | deep intronic (+276 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.49 | GERP -1.6, phastCons 0.022 |
| Non-coding constraint | Z -0.23 | 1 kb window · o/e 1.02 · regional · uncalibrated |
| Overall | ||
| CADD | 1.736 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.67%
African / African-American · 1,109/41,536 alleles
Filtering AF
2.54%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.49%
Overall
0.769%
1,171/152,240 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.67% | 37 |
| Middle Eastern | 0.34% | 294 |
| Admixed American | 0.34% | 294 |
| Remaining individualsnot grpmax-eligible | 0.237% | 423 |
| South Asian | 0.0207% | 4,824 |
| European (non-Finnish) | 0.00441% | 22,666 |
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+276del
- MANE Select
- NM_005050
- dbSNP
- rs538530917
- Type
- Deletion
- Location
- chr14:74302599 (GRCh38)
- Gene constraint
- LOEUF 0.772 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.18 · 4 PDB
Similar variants
- ABCD4 p.Ala237fs Likely pathogenic ★★ same type
- ABCD4 p.Trp377fs Pathogenic ★★ same type
- ABCD4 c.669-11_669-8del Benign ★★ same type
- ABCD4 p.Arg125fs Pathogenic ★ same type
- ABCD4 p.Arg432fs Pathogenic ★ same type
- ABCD4 p.Gln101fs Likely pathogenic ★ same type
- ABCD4 p.Gln215fs Pathogenic ★ same type
- ABCD4 p.Gly183_Trp184insTer Pathogenic ★ 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-276del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown