Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 51.4%, 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 | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -3.7 |
| Overall | ||
| CADD | 0.155 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
51.4%
African / African-American · 38,078/74,098 alleles
Filtering AF
51%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 50.8%
Overall
18.4%
292,180/1,587,048 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 51.4% | 2 |
| East Asian | 45.5% | 2 |
| South Asian | 33.9% | 3 |
| Admixed American | 25.3% | 4 |
| Middle Eastern | 21.1% | 5 |
| Ashkenazi Jewishnot grpmax-eligible | 20.6% | 5 |
| Remaining individualsnot grpmax-eligible | 20.6% | 5 |
| Finnishnot grpmax-eligible | 15.8% | 6 |
| European (non-Finnish) | 13.8% | 7 |
| Amishnot grpmax-eligible | 13% | 8 |
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
- DMBT1
- Protein
- p.Ser781=
- Coding
- c.2343G>A
- MANE Select
- NM_001377530
- dbSNP
- rs4752722
- Type
- single nucleotide variant
- Location
- chr10:122592438 (GRCh38)
- Gene constraint
- LOEUF 0.904 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.29 · 6 PDB
- Residue 781
- a disulfide bond; the srcr 6 domain
Similar variants
- DMBT1 p.Ser781Leu Uncertain significance ★ ⚠ same residue
- DMBT1 p.Asp696Val Uncertain significance ★★ ⚠ same type
- DMBT1 p.His805Asn Uncertain significance ★★ ⚠ same type
- DMBT1 p.Arg670Cys Benign ★★ ⚠ same type
- DMBT1 p.Asp1796Glu Benign ★★ ⚠ same type
- DMBT1 p.Asp635Asn Benign ★★ ⚠ same type
- DMBT1 p.Asp668Asn Benign ★★ ⚠ same type
- DMBT1 p.Asp696= Likely benign ★★ 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/dmbt1-p-ser781 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown