PHF2 p.Thr992=
c.2976C>A · rs10992856 · VCV2659316
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.144%, mid)
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 -1.9 | GERP -3.1 |
| Overall | ||
| CADD | 5.807 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.144%
Middle Eastern · 4/2,778 alleles
Filtering AF
0.0703%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0624%
Overall
0.0615%
348/565,916 alleles · rare
exomes 336/529,958 · genomes 12/35,958 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.144% | 695 |
| African / African-American | 0.11% | 905 |
| Finnishnot grpmax-eligible | 0.0962% | 1,040 |
| European (non-Finnish) | 0.0721% | 1,387 |
| East Asian | 0.0327% | 3,055 |
| Remaining individualsnot grpmax-eligible | 0.0245% | 4,074 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0239% | 4,179 |
| South Asian | 0.0165% | 6,045 |
| Admixed American | 0.0132% | 7,551 |
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
- PHF2
- Protein
- p.Thr992=
- Coding
- c.2976C>A
- MANE Select
- NM_005392
- dbSNP
- rs10992856
- Type
- single nucleotide variant
- Location
- chr9:93676737 (GRCh38)
- Gene constraint
- LOEUF 0.329 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 62.14 · 9 PDB
- Residue 992
- the 'disordered' region
Similar variants
- PHF2 c.299+7T>A Benign ★★ same type
- PHF2 c.789+10G>A Benign/Likely benign ★★ same type
- PHF2 p.Asp103= Benign ★★ same type
- PHF2 p.Leu645= Benign/Likely benign ★★ same type
- PHF2 p.Pro786= Benign ★★ same type
- PHF2 p.Pro988= Benign ★★ same type
- PHF2 p.Ser725= Benign ★★ same type
- PHF2 p.Ser738= Benign ★★ 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/phf2-p-thr992 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown