ABCC1 p.Ala1406=
c.4218C>T · rs34526519 · VCV775039
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.94%, afr)
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 -7.1 | GERP -3.6 |
| Overall | ||
| CADD | 1.017 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.94%
African / African-American · 1,453/75,036 alleles
Filtering AF
1.85%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.82%
Overall
0.167%
2,694/1,614,148 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.94% | 52 |
| Middle Eastern | 0.759% | 132 |
| Admixed American | 0.353% | 283 |
| Remaining individualsnot grpmax-eligible | 0.283% | 353 |
| Ashkenazi Jewishnot grpmax-eligible | 0.179% | 559 |
| European (non-Finnish) | 0.0625% | 1,601 |
| South Asian | 0.0176% | 5,692 |
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
- ABCC1
- Protein
- p.Ala1406=
- Coding
- c.4218C>T
- MANE Select
- NM_004996
- dbSNP
- rs34526519
- Type
- single nucleotide variant
- Location
- chr16:16136570 (GRCh38)
- Gene constraint
- LOEUF 0.564 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.01 · 5 PDB
- Residue 1406
- the abc transporter 2 domain
Similar variants
- ABCC1 p.Thr1464Met Uncertain significance ★★ ⚠ same type
- ABCC1 c.1381-5C>G Benign ★★ same type
- ABCC1 p.Ala1260= Benign ★★ same type
- ABCC1 p.Arg433Ser Benign ★★ same type
- ABCC1 p.Asp637= Likely benign ★★ same type
- ABCC1 p.Gly762= Benign/Likely benign ★★ same type
- ABCC1 p.Gly885= Benign ★★ same type
- ABCC1 p.Ile1484= Benign ★★ 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/abcc1-p-ala1406 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown