DLD c.875+281T>C
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 11.7%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +281 | deep intronic (+281 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.63 | GERP -0.063, phastCons 0.048 |
| Non-coding constraint | Z 0.92 | 1 kb window · o/e 0.93 · regional · uncalibrated |
| Overall | ||
| CADD | 4.731 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
11.7%
African / African-American · 4,855/41,508 alleles
Filtering AF
11.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 11.3%
Overall
3.38%
5,149/152,210 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 11.7% | 9 |
| Remaining individualsnot grpmax-eligible | 3.03% | 33 |
| Admixed American | 1.24% | 80 |
| Middle Eastern | 1.02% | 98 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0866% | 1,155 |
| European (non-Finnish) | 0.0471% | 2,125 |
| South Asian | 0.0207% | 4,824 |
| East Asian | 0.0193% | 5,190 |
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.875+281T>C
- MANE Select
- NM_000108
- dbSNP
- rs79144899
- Type
- single nucleotide variant
- Location
- chr7:107915977 (GRCh38)
- Gene constraint
- LOEUF 0.727 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.69 · 17 PDB
Similar variants
- DLD c.1464+1G>A Pathogenic/Likely pathogenic ★★ same type
- DLD c.198+1G>T Likely pathogenic ★★ same type
- DLD c.39+1G>A Likely pathogenic ★★ same type
- DLD c.40-2A>G Likely pathogenic ★★ same type
- DLD c.583-1G>C Likely pathogenic ★★ same type
- DLD c.684+1G>T Likely pathogenic ★★ same type
- DLD c.875+1G>A Pathogenic/Likely pathogenic ★★ same type
- DLD p.Arg315Ter 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-875-plus-281t-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown