DBT c.*6903del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 95.7%, eas) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Non-coding constraint | Z 1.58 | 1 kb window · o/e 0.88 · regional · uncalibrated |
| Overall | ||
| CADD | 1.581 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
95.7%
East Asian · 4,729/4,942 alleles
Filtering AF
93.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 92.5%
Overall
82.7%
118,636/143,486 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 95.7% | 1 |
| South Asian | 92.4% | 1 |
| Middle Eastern | 89.8% | 1 |
| Admixed American | 88.3% | 1 |
| Finnishnot grpmax-eligible | 87.1% | 1 |
| European (non-Finnish) | 85.7% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 85.6% | 1 |
| Remaining individualsnot grpmax-eligible | 85.2% | 1 |
| Amishnot grpmax-eligible | 80.2% | 1 |
| African / African-American | 71.2% | 1 |
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
- DBT
- Coding
- c.*6903del
- MANE Select
- NM_001918
- dbSNP
- rs71709231
- Type
- Deletion
- Location
- chr1:100189352 (GRCh38)
- Gene constraint
- LOEUF 1.255 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 78.71 · 5 PDB
Similar variants
- DBT c.434-15_434-4del Pathogenic/Likely pathogenic ★★ same type
- DBT p.Cys26fs Pathogenic ★★ same type
- DBT p.Lys120fs Pathogenic ★★ same type
- DBT p.Phe276fs Pathogenic/Likely pathogenic ★★ same type
- DBT p.Pro238fs Pathogenic ★★ same type
- DBT p.Thr153fs Pathogenic/Likely pathogenic ★★ same type
- DBT p.Thr388_Thr389insTer Likely pathogenic ★★ same type
- DBT p.Thr91fs 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/dbt-c-star-6903del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown