ABCC12 p.Phe54=
c.162C>T · rs60702908 · VCV775043
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 9.85%, afr) — too common for a highly-penetrant pathogenic allele
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 -8.4 | GERP -4.8 |
| Overall | ||
| CADD | 0.199 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
9.85%
African / African-American · 7,387/75,026 alleles
Filtering AF
9.66%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9.58%
Overall
0.525%
8,471/1,614,132 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 9.85% | 10 |
| Remaining individualsnot grpmax-eligible | 0.73% | 137 |
| Admixed American | 0.698% | 143 |
| Middle Eastern | 0.297% | 337 |
| South Asian | 0.0209% | 4,793 |
| European (non-Finnish) | 0.0142% | 7,066 |
| East Asian | 0.00891% | 11,222 |
| Finnishnot grpmax-eligible | 0.00156% | 64,044 |
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.Phe54=
- Coding
- c.162C>T
- MANE Select
- NM_001393797
- dbSNP
- rs60702908
- Type
- single nucleotide variant
- Location
- chr16:48144023 (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.Arg122= Likely benign ★★ 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.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-phe54 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown