ABCC12 p.Ser993=
c.2979C>T · rs41280921 · VCV2646496
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.502%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.207 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.72 | GERP -3.8, phastCons 0.001 |
| Overall | ||
| CADD | 0.682 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.502%
European (non-Finnish) · 5,920/1,180,044 alleles
Filtering AF
0.491%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.487%
Overall
0.393%
6,336/1,614,250 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.502% | 199 |
| Middle Eastern | 0.231% | 433 |
| Remaining individualsnot grpmax-eligible | 0.229% | 437 |
| Finnishnot grpmax-eligible | 0.201% | 496 |
| Admixed American | 0.115% | 870 |
| African / African-American | 0.0746% | 1,341 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00675% | 14,804 |
| South Asian | 0.00329% | 30,360 |
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.Ser993=
- Coding
- c.2979C>T
- MANE Select
- NM_001393797
- dbSNP
- rs41280921
- Type
- single nucleotide variant
- Location
- chr16:48100931 (GRCh38)
- Gene constraint
- LOEUF 1.022 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.09
- Residue 993
- the abc transmembrane type-1 2 domain
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.Phe54= 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/abcc12-p-ser993 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown