ABCC2 p.Phe71=
c.213C>T · rs770824435 · VCV595862
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0147%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.33 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3 | GERP -5.1 |
| Overall | ||
| CADD | 11.99 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0147%
African / African-American · 11/74,908 alleles
Filtering AF
0.00816%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00633%
Overall
0.00161%
26/1,613,810 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0147% | 6,810 |
| South Asian | 0.00329% | 30,360 |
| European (non-Finnish) | 0.00102% | 98,327 |
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.Phe71=
- Coding
- c.213C>T
- MANE Select
- NM_000392
- dbSNP
- rs770824435
- Type
- single nucleotide variant
- Location
- chr10:99792239 (GRCh38)
- Gene constraint
- LOEUF 0.985 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.40 · 16 PDB
- Residue 71
- an α-helix
Similar variants
- 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
- ABCC2 c.3741+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-phe71 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown