DMRTA2 p.Ala396=
c.1188C>T · rs2746610 · VCV1337081
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 95.3%, 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 0.71 | GERP -1.3, phastCons 0.84 |
| Overall | ||
| CADD | 1.888 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
95.3%
African / African-American · 57,945/60,776 alleles
Filtering AF
94.7%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 94.4%
Overall
84.8%
939,655/1,108,520 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 95.3% | 1 |
| Admixed American | 89.6% | 1 |
| Finnishnot grpmax-eligible | 88.9% | 1 |
| Middle Eastern | 85.9% | 1 |
| Amishnot grpmax-eligible | 85.5% | 1 |
| Remaining individualsnot grpmax-eligible | 84.6% | 1 |
| European (non-Finnish) | 83.9% | 1 |
| East Asian | 83.7% | 1 |
| South Asian | 82.9% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 82% | 1 |
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
- DMRTA2
- Protein
- p.Ala396=
- Coding
- c.1188C>T
- MANE Select
- NM_032110
- dbSNP
- rs2746610
- Type
- single nucleotide variant
- Location
- chr1:50419106 (GRCh38)
- Gene constraint
- LOEUF 1.236 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 57.64
Similar variants
- DMRTA2 p.Ala396Ser Uncertain significance ★ ⚠ same residue
- DMRTA2 p.Ala396_Ala397del Benign ★ same residue
- DMRTA2 p.Leu406Gln Uncertain significance ★★ ⚠ same type
- DMRTA2 p.Ala394= Benign ★★ same type
- DMRTA2 p.Ser477Asn Benign/Likely benign ★★ ⚠ same type
- DMRTA2 p.Ala144Thr Uncertain significance ★ ⚠ same type
- DMRTA2 p.Ala14Glu Uncertain significance ★ ⚠ same type
- DMRTA2 p.Ala253Pro 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/dmrta2-p-ala396 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown