ACP2 p.Leu165=
c.495G>A · rs10838677 · VCV558906
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 11.3%, sas) — 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 0.078 | GERP -0.045, phastCons 0.91 |
| Overall | ||
| CADD | 8.477 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
11.3%
South Asian · 10,302/91,086 alleles
Filtering AF
11.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 11.1%
Overall
3.96%
63,859/1,614,214 alleles · common
exomes 58,666/1,461,888 · genomes 5,193/152,326 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 11.3% | 9 |
| Finnishnot grpmax-eligible | 4.95% | 20 |
| Remaining individualsnot grpmax-eligible | 4.13% | 24 |
| European (non-Finnish) | 3.64% | 27 |
| East Asian | 3.61% | 28 |
| Middle Eastern | 2.87% | 35 |
| African / African-American | 2.3% | 43 |
| Amishnot grpmax-eligible | 2.3% | 43 |
| Admixed American | 1.45% | 69 |
| Ashkenazi Jewishnot grpmax-eligible | 1.3% | 77 |
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
- ACP2
- Protein
- p.Leu165=
- Coding
- c.495G>A
- MANE Select
- NM_001610
- dbSNP
- rs10838677
- Type
- single nucleotide variant
- Location
- chr11:47245528 (GRCh38)
- Gene constraint
- LOEUF 0.804 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.09
Similar variants
- ACP2 c.856-4G>A Benign ★★ same type
- ACP2 p.Arg10Trp Likely benign ★★ same type
- ACP2 p.Phe393Leu Benign/Likely benign ★★ same type
- ACP2 p.Val416= Benign ★★ same type
- ACP2 p.Ala11Glu Uncertain significance ★ ⚠ same type
- ACP2 p.Ala272Val Uncertain significance ★ ⚠ same type
- ACP2 p.Ala336Thr Uncertain significance ★ ⚠ same type
- ACP2 p.Ala336Val 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/acp2-p-leu165 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown