Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 66.5%, eas) — 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 1.2 | GERP -3.1, phastCons 1 |
| Overall | ||
| CADD | 7.279 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
66.5%
East Asian · 29,746/44,718 alleles
Filtering AF
65.9%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 65.6%
Overall
31.5%
507,201/1,611,918 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 66.5% | 2 |
| South Asian | 39.1% | 3 |
| African / African-American | 37.7% | 3 |
| Amishnot grpmax-eligible | 33.5% | 3 |
| Remaining individualsnot grpmax-eligible | 32.1% | 3 |
| Middle Eastern | 31.4% | 3 |
| European (non-Finnish) | 30.2% | 3 |
| Ashkenazi Jewishnot grpmax-eligible | 26.5% | 4 |
| Finnishnot grpmax-eligible | 23.4% | 4 |
| Admixed American | 20.6% | 5 |
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
- DNAL4
- Protein
- p.Asp12=
- Coding
- c.36T>C
- MANE Select
- NM_005740
- dbSNP
- rs760482
- Type
- single nucleotide variant
- Location
- chr22:38782696 (GRCh38)
- Gene constraint
- LOEUF 1.443 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.49
Similar variants
- DNAL4 p.Ala53Asp Uncertain significance ★ ⚠ same type
- DNAL4 p.Ala98Val Uncertain significance ★ ⚠ same type
- DNAL4 p.Arg15Gln Uncertain significance ★ ⚠ same type
- DNAL4 p.Arg32Ser Uncertain significance ★ ⚠ same type
- DNAL4 p.Glu30Asp Uncertain significance ★ ⚠ same type
- DNAL4 p.Leu21Val Uncertain significance ★ ⚠ same type
- DNAL4 p.Met31Val Uncertain significance ★ ⚠ same type
- DNAL4 p.Met56Val 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/dnal4-p-asp12 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown