DHX57 p.Phe1322=
c.3966C>T · rs146662521 · VCV2650842
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.99%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.079 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.4 | GERP -5.1 |
| Overall | ||
| CADD | 2.944 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.99%
South Asian · 902/91,072 alleles
Filtering AF
0.937%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.915%
Overall
0.283%
4,575/1,614,100 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.99% | 101 |
| Middle Eastern | 0.66% | 152 |
| Remaining individualsnot grpmax-eligible | 0.296% | 338 |
| European (non-Finnish) | 0.281% | 356 |
| Admixed American | 0.113% | 882 |
| African / African-American | 0.0506% | 1,975 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0439% | 2,277 |
| Finnishnot grpmax-eligible | 0.0141% | 7,112 |
| East Asian | 0.00223% | 44,886 |
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
- DHX57
- Protein
- p.Phe1322=
- Coding
- c.3966C>T
- MANE Select
- NM_198963
- dbSNP
- rs146662521
- Type
- single nucleotide variant
- Location
- chr2:38802766 (GRCh38)
- Gene constraint
- LOEUF 0.742 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 76.68
Similar variants
- DHX57 p.Ala1014Val Uncertain significance ★ ⚠ same type
- DHX57 p.Ala1084Thr Uncertain significance ★ ⚠ same type
- DHX57 p.Ala1115Val Uncertain significance ★ ⚠ same type
- DHX57 p.Ala1117Gly Uncertain significance ★ ⚠ same type
- DHX57 p.Ala1117Ser Uncertain significance ★ ⚠ same type
- DHX57 p.Ala1127Val Uncertain significance ★ ⚠ same type
- DHX57 p.Ala1207Thr Uncertain significance ★ ⚠ same type
- DHX57 p.Ala125Asp 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/dhx57-p-phe1322 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown