ABCA1 c.2115+84del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.54%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +84 | deep intronic (+84 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.029 | GERP -1.4 |
| Non-coding constraint | Z 3.13 | 1 kb window · o/e 0.78 · regional · uncalibrated |
| Overall | ||
| CADD | 0.205 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.54%
African / African-American · 1,758/69,300 alleles
Filtering AF
2.44%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.4%
Overall
0.143%
1,987/1,385,312 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.54% | 39 |
| Admixed American | 0.188% | 532 |
| Remaining individualsnot grpmax-eligible | 0.174% | 573 |
| Middle Eastern | 0.135% | 738 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00361% | 27,708 |
| European (non-Finnish) | 0.00251% | 39,839 |
| Finnishnot grpmax-eligible | 0.00175% | 57,100 |
| South Asian | 0.00123% | 81,570 |
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
- Coding
- c.2115+84del
- MANE Select
- NM_005502
- dbSNP
- rs559207960
- Type
- Deletion
- Location
- chr9:104828832 (GRCh38)
- Gene constraint
- LOEUF 0.563 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.50 · 7 PDB
Similar variants
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- ABCA1 c.6309-16_6309-15del Likely benign ★★ same type
- ABCA1 c.6309-20del Likely benign ★★ same type
- ABCA1 c.721-10del Benign ★★ same type
- ABCA1 p.Asn141fs Pathogenic ★ same type
- ABCA1 p.Asp1156fs Likely 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/abca1-c-2115-plus-84del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown