Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 70.2%, 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 0.13 | GERP -2.1, phastCons 0.001 |
| Overall | ||
| CADD | 3.514 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
70.2%
African / African-American · 39,938/56,915 alleles
Filtering AF
69.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 69.4%
Overall
15%
181,296/1,208,022 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 70.2% | 1 |
| Admixed American | 21.4% | 5 |
| South Asian | 16.9% | 6 |
| Remaining individualsnot grpmax-eligible | 16.1% | 6 |
| Finnishnot grpmax-eligible | 14.9% | 7 |
| European (non-Finnish) | 11.4% | 9 |
| East Asian | 10.4% | 10 |
| Middle Eastern | 8.8% | 11 |
| Ashkenazi Jewishnot grpmax-eligible | 6.35% | 16 |
| Amishnot grpmax-eligible | 0.877% | 114 |
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
- DNASE1L1
- Protein
- p.Pro67=
- Coding
- c.201G>C
- MANE Select
- NM_001303620
- dbSNP
- rs1130929
- Type
- single nucleotide variant
- Location
- chrX:154405018 (GRCh38)
- Structure
- AlphaFold pLDDT 90.83
Similar variants
- TAFAZZIN c.109+5G>A Pathogenic/Likely pathogenic ★★ same type
- TAFAZZIN c.109+5G>C Likely pathogenic ★★ same type
- TAFAZZIN p.Gly29Arg Uncertain significance ★★ ⚠ same type
- TAFAZZIN p.Met39Val Uncertain significance ★★ ⚠ same type
- TAFAZZIN p.Pro10Arg Uncertain significance ★★ ⚠ same type
- TAFAZZIN p.Pro13Ser Uncertain significance ★★ ⚠ same type
- TAFAZZIN p.Trp17Cys Uncertain significance ★★ ⚠ same type
- TAFAZZIN p.Leu19= 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/dnase1l1-p-pro67 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown