DIAPH2 p.Phe504=
c.1512C>T · rs143029608 · VCV715210
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.11%, afr)
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>A here scores Δ0.40 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -3.5 |
| Overall | ||
| CADD | 0.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.11%
African / African-American · 1,181/56,059 alleles
Filtering AF
2.01%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.97%
Overall
0.135%
1,586/1,176,431 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.11% | 47 |
| Middle Eastern | 0.307% | 326 |
| Admixed American | 0.192% | 520 |
| Remaining individualsnot grpmax-eligible | 0.164% | 610 |
| South Asian | 0.0359% | 2,785 |
| Finnishnot grpmax-eligible | 0.026% | 3,844 |
| European (non-Finnish) | 0.0229% | 4,358 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00467% | 21,396 |
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
- DIAPH2
- Protein
- p.Phe504=
- Coding
- c.1512C>T
- MANE Select
- NM_006729
- dbSNP
- rs143029608
- Type
- single nucleotide variant
- Location
- chrX:96948937 (GRCh38)
- Structure
- AlphaFold pLDDT 76.09
Similar variants
- DIAPH2 p.Ala83Thr Benign/Likely benign ★★ same type
- DIAPH2 p.Ile475= Likely benign ★★ same type
- DIAPH2 c.733-1G>T Uncertain significance ★ same type
- DIAPH2 p.Ala125Val Uncertain significance ★ ⚠ same type
- DIAPH2 p.Ala488Val Uncertain significance ★ ⚠ same type
- DIAPH2 p.Ala672Thr Uncertain significance ★ ⚠ same type
- DIAPH2 p.Ala6Thr Uncertain significance ★ ⚠ same type
- DIAPH2 p.Ala870Glu 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/diaph2-p-phe504 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown