Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 59.7%, sas) — 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 3.5 | GERP -0.018, phastCons 1 |
| Overall | ||
| CADD | 10.34 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
59.7%
South Asian · 54,419/91,078 alleles
Filtering AF
59.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 59.2%
Overall
51.3%
827,444/1,611,764 alleles · common
exomes 755,394/1,459,710 · genomes 72,050/152,054 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 59.7% | 2 |
| Middle Eastern | 59.3% | 2 |
| Finnishnot grpmax-eligible | 53.6% | 2 |
| European (non-Finnish) | 52.1% | 2 |
| Remaining individualsnot grpmax-eligible | 50.8% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 49.6% | 2 |
| Admixed American | 46.9% | 2 |
| East Asian | 45.9% | 2 |
| Amishnot grpmax-eligible | 45.3% | 2 |
| African / African-American | 34% | 3 |
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
- DVL2
- Protein
- p.Ser207=
- Coding
- c.621C>T
- MANE Select
- NM_004422
- dbSNP
- rs222836
- Type
- single nucleotide variant
- Location
- chr17:7229843 (GRCh38)
- Gene constraint
- LOEUF 0.719 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 59.37 · 16 PDB
- Residue 207
- the 'disordered' region
Similar variants
- DVL2 c.1035-8C>T Benign ★★ same type
- DVL2 c.1544-16T>C Benign ★★ same type
- DVL2 p.Gln554= Benign ★★ same type
- DVL2 p.Leu317= Benign ★★ same type
- DVL2 p.Thr250= Likely benign ★★ same type
- DVL2 p.Ala114Val Uncertain significance ★ ⚠ same type
- DVL2 p.Ala384Val Uncertain significance ★ ⚠ same type
- DVL2 p.Ala385Thr Uncertain significance ★ ⚠ 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/dvl2-p-ser207 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown