DLD c.*295del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.1%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.7 | GERP -3.5 |
| Non-coding constraint | Z 1.73 | 1 kb window · o/e 0.83 · regional · uncalibrated |
| Overall | ||
| CADD | 1.979 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.1%
African / African-American · 1,356/43,782 alleles
Filtering AF
2.96%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.9%
Overall
0.59%
1,449/245,562 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.1% | 32 |
| Admixed American | 0.292% | 342 |
| Remaining individualsnot grpmax-eligible | 0.279% | 359 |
| Middle Eastern | 0.15% | 668 |
| South Asian | 0.021% | 4,755 |
| European (non-Finnish) | 0.0078% | 12,827 |
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
- DLD
- Coding
- c.*295del
- MANE Select
- NM_000108
- dbSNP
- rs139767397
- Type
- Deletion
- Location
- chr7:107919551 (GRCh38)
- Gene constraint
- LOEUF 0.727 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.69 · 17 PDB
Similar variants
- DLD p.Gln268fs Pathogenic/Likely pathogenic ★★ same type
- DLD p.Gly137del Pathogenic/Likely pathogenic ★★ same type
- DLD p.Gly246fs Likely pathogenic ★★ same type
- DLD p.Thr34_Tyr35insTer Pathogenic/Likely pathogenic ★★ same type
- DLD p.Tyr473fs Pathogenic ★★ same type
- DLD p.Asp121fs Pathogenic ★ same type
- DLD p.Asp286fs Likely pathogenic ★ same type
- DLD p.Asp368fs 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/dld-c-star-295del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown