DDHD2 c.*28C>T
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0915%, 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 Δ0.39 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.1 | GERP -4.6 |
| Non-coding constraint | Z 0.02 | 1 kb window · o/e 1.00 · regional · uncalibrated |
| Overall | ||
| CADD | 1.673 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0915%
African / African-American · 38/41,548 alleles
Filtering AF
0.0685%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0605%
Overall
0.0276%
42/152,256 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0915% | 1,093 |
| East Asian | 0.0192% | 5,216 |
| Admixed American | 0.00647% | 15,454 |
| European (non-Finnish) | 0.00291% | 34,336 |
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
- DDHD2
- Coding
- c.*28C>T
- MANE Select
- NM_015214
- dbSNP
- rs145138059
- Type
- single nucleotide variant
- Location
- chr8:38260601 (GRCh38)
- Gene constraint
- LOEUF 0.758 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.70
Similar variants
- DDHD2 c.1126-2A>G Likely pathogenic ★★ same type
- DDHD2 c.1248+2T>C Likely pathogenic ★★ same type
- DDHD2 p.Arg232Ter Pathogenic ★★ same type
- DDHD2 p.Arg329Ter Pathogenic ★★ same type
- DDHD2 p.Arg422Ter Likely pathogenic ★★ same type
- DDHD2 p.Arg516Ter Pathogenic ★★ same type
- DDHD2 p.Asp660His Pathogenic/Likely pathogenic ★★ same type
- DDHD2 p.Gln286Ter Pathogenic/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/ddhd2-c-star-28c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown