DNAI3 p.Asp672=
c.2016C>T · rs138281012 · VCV771117
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.7%, sas)
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 -1.9 | GERP -3.1 |
| Overall | ||
| CADD | 1.614 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.7%
South Asian · 2,462/91,078 alleles
Filtering AF
2.61%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.58%
Overall
0.268%
4,330/1,614,184 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 2.7% | 37 |
| Middle Eastern | 0.445% | 225 |
| Remaining individualsnot grpmax-eligible | 0.341% | 293 |
| European (non-Finnish) | 0.129% | 774 |
| Ashkenazi Jewishnot grpmax-eligible | 0.115% | 871 |
| Admixed American | 0.055% | 1,819 |
| African / African-American | 0.0346% | 2,886 |
| Finnishnot grpmax-eligible | 0.0125% | 8,005 |
| East Asian | 0.00668% | 14,961 |
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
- DNAI3
- Protein
- p.Asp672=
- Coding
- c.2016C>T
- MANE Select
- NM_145172
- dbSNP
- rs138281012
- Type
- single nucleotide variant
- Location
- chr1:85124155 (GRCh38)
- Gene constraint
- LOEUF 0.879 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.17 · 1 PDB
Similar variants
- DNAI3 c.1350+6C>A Benign ★★ same type
- DNAI3 p.Ala308Thr Benign ★★ same type
- DNAI3 p.Arg79= Benign ★★ same type
- DNAI3 p.Asp577= Benign ★★ same type
- DNAI3 p.Glu458= Likely benign ★★ same type
- DNAI3 p.Glu751= Benign ★★ same type
- DNAI3 p.His788= Benign ★★ same type
- DNAI3 p.His817= 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/dnai3-p-asp672 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown