PML p.Ala264=
c.792C>T · rs17849259 · VCV774496
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.874%, nfe)
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 -4.3 | GERP -3.5 |
| Overall | ||
| CADD | 5.791 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.874%
European (non-Finnish) · 10,295/1,178,490 alleles
Filtering AF
0.859%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.854%
Overall
0.703%
11,293/1,607,302 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.874% | 114 |
| Remaining individualsnot grpmax-eligible | 0.607% | 165 |
| Admixed American | 0.378% | 264 |
| Finnishnot grpmax-eligible | 0.32% | 312 |
| Ashkenazi Jewishnot grpmax-eligible | 0.302% | 331 |
| African / African-American | 0.14% | 714 |
| Middle Eastern | 0.0165% | 6,046 |
| South Asian | 0.0088% | 11,360 |
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
- PML
- Protein
- p.Ala264=
- Coding
- c.792C>T
- MANE Select
- NM_033238
- dbSNP
- rs17849259
- Type
- single nucleotide variant
- Location
- chr15:74023017 (GRCh38)
- Gene constraint
- LOEUF 0.613 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 71.17 · 20 PDB
Similar variants
- PML c.1710+1245A>G Benign ★★ same type
- PML c.1710+1270G>T Benign ★★ same type
- PML c.1710+1705A>G Benign ★★ same type
- PML c.1710+813G>A Benign ★★ same type
- PML p.Ala675= Benign ★★ same type
- PML p.Pro761= Benign ★★ same type
- PML p.Pro791= Benign/Likely benign ★★ same type
- PML c.1710+1152C>T 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/pml-p-ala264 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown