ABCC12 p.Arg122=
c.366C>T · rs566970228 · VCV2646497
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0472%, sas)
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 -8.3 | GERP -4.4 |
| Overall | ||
| CADD | 0.089 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0472%
South Asian · 43/91,086 alleles
Filtering AF
0.036%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0321%
Overall
0.00756%
122/1,614,200 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0472% | 2,118 |
| Middle Eastern | 0.033% | 3,031 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,209 |
| Admixed American | 0.0117% | 8,576 |
| European (non-Finnish) | 0.00475% | 21,072 |
| African / African-American | 0.00267% | 37,518 |
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
- ABCC12
- Protein
- p.Arg122=
- Coding
- c.366C>T
- MANE Select
- NM_001393797
- dbSNP
- rs566970228
- Type
- single nucleotide variant
- Location
- chr16:48141263 (GRCh38)
- Gene constraint
- LOEUF 1.022 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.09
Similar variants
- ABCC12 p.Thr1080Ala Uncertain significance ★★ ⚠ same type
- ABCC12 p.Gln831Ter Likely benign ★★ same type
- ABCC12 p.Glu1191Ala Benign ★★ same type
- ABCC12 p.Gly164Ter Benign/Likely benign ★★ same type
- ABCC12 p.Lys1344= Benign ★★ same type
- ABCC12 p.Lys894Met Benign ★★ same type
- ABCC12 p.Phe54= Benign ★★ same type
- ABCC12 p.Ala1312Thr 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/abcc12-p-arg122 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown