DHX16 p.Val962=
c.2886G>C · rs146265602 · VCV711864
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.26%, 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 -0.41 | phastCons 0.035 |
| Overall | ||
| CADD | 2.758 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.26%
Middle Eastern · 137/6,060 alleles
Filtering AF
1.95%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.84%
Overall
0.257%
4,139/1,613,036 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 2.26% | 44 |
| Ashkenazi Jewishnot grpmax-eligible | 1.26% | 79 |
| Remaining individualsnot grpmax-eligible | 0.386% | 259 |
| Admixed American | 0.35% | 286 |
| South Asian | 0.257% | 389 |
| European (non-Finnish) | 0.24% | 417 |
| Finnishnot grpmax-eligible | 0.116% | 862 |
| African / African-American | 0.0493% | 2,028 |
| East Asian | 0.00223% | 44,880 |
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
- DHX16
- Protein
- p.Val962=
- Coding
- c.2886G>C
- MANE Select
- NM_003587
- dbSNP
- rs146265602
- Type
- single nucleotide variant
- Location
- chr6:30654817 (GRCh38)
- Gene constraint
- LOEUF 0.716 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.82 · 12 PDB
- Residue 962
- a turn
Similar variants
- DHX16 p.Thr674Met Pathogenic/Likely pathogenic ★★ same type
- DHX16 p.Arg940Cys Uncertain significance ★★ ⚠ same type
- DHX16 p.Arg956Gln Uncertain significance ★★ ⚠ same type
- DHX16 p.Asp580Gly Uncertain significance ★★ ⚠ same type
- DHX16 p.Glu105Lys Uncertain significance ★★ ⚠ same type
- DHX16 p.Glu995Gly Uncertain significance ★★ ⚠ same type
- DHX16 c.207+8C>G Benign/Likely benign ★★ same type
- DHX16 p.Asp520Asn Likely pathogenic ★ 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/dhx16-p-val962 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown