DLD c.337+154A>C
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.74%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +154 | deep intronic (+154 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.61 | GERP -2.2 |
| Non-coding constraint | Z 0.16 | 1 kb window · o/e 0.99 · regional · uncalibrated |
| Overall | ||
| CADD | 6.375 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.74%
African / African-American · 1,419/51,750 alleles
Filtering AF
2.62%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.58%
Overall
0.289%
1,505/520,838 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.74% | 36 |
| Remaining individualsnot grpmax-eligible | 0.19% | 526 |
| Admixed American | 0.113% | 882 |
| Middle Eastern | 0.0358% | 2,792 |
| European (non-Finnish) | 0.00208% | 48,090 |
| South Asian | 0.00204% | 49,018 |
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.337+154A>C
- MANE Select
- NM_000108
- dbSNP
- rs149266807
- Type
- single nucleotide variant
- Location
- chr7:107903701 (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-337-plus-154a-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown