ABCC2 p.Tyr172=
c.516C>T · rs766116167 · VCV2428308
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0117%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.54 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.4 | GERP -5.2, phastCons 0.001 |
| Overall | ||
| CADD | 5.607 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0117%
Admixed American · 7/59,990 alleles
Filtering AF
0.00543%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00381%
Overall
0.00149%
24/1,613,762 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0117% | 8,570 |
| East Asian | 0.00446% | 22,446 |
| African / African-American | 0.00267% | 37,456 |
| South Asian | 0.0022% | 45,543 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,480 |
| European (non-Finnish) | 0.000848% | 117,988 |
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
- ABCC2
- Protein
- p.Tyr172=
- Coding
- c.516C>T
- MANE Select
- NM_000392
- dbSNP
- rs766116167
- Type
- single nucleotide variant
- Location
- chr10:99793939 (GRCh38)
- Gene constraint
- LOEUF 0.985 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.40 · 16 PDB
- Residue 172
- an α-helix
Similar variants
- ABCC2 p.Tyr172fs Pathogenic ★ same residue
- ABCC2 c.1031+4A>G Pathogenic/Likely pathogenic ★★ same type
- ABCC2 c.1967+1G>A Pathogenic/Likely pathogenic ★★ same type
- ABCC2 c.1968-1G>C Pathogenic/Likely pathogenic ★★ same type
- ABCC2 c.3258+1G>A Pathogenic/Likely pathogenic ★★ same type
- ABCC2 c.333+1G>A Likely pathogenic ★★ same type
- ABCC2 c.3414+1G>A Likely pathogenic ★★ same type
- ABCC2 c.3415-1G>A Pathogenic/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/abcc2-p-tyr172 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown