Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 9.13%, 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 -0.59 | GERP -2.3, phastCons 0.025 |
| Overall | ||
| CADD | 9.106 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
9.13%
African / African-American · 6,844/74,994 alleles
Filtering AF
8.95%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 8.87%
Overall
0.49%
7,912/1,614,120 alleles · common
exomes 3,880/1,461,874 · genomes 4,032/152,246 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 9.13% | 11 |
| Admixed American | 0.736% | 136 |
| Remaining individualsnot grpmax-eligible | 0.642% | 156 |
| Middle Eastern | 0.544% | 184 |
| South Asian | 0.0307% | 3,253 |
| European (non-Finnish) | 0.0138% | 7,239 |
| Finnishnot grpmax-eligible | 0.00156% | 64,034 |
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
- PRDM9
- Protein
- p.Asp30=
- Coding
- c.90C>T
- MANE Select
- NM_020227
- dbSNP
- rs7714612
- Type
- single nucleotide variant
- Location
- chr5:23509490 (GRCh38)
- Gene constraint
- LOEUF 1.039 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.19 · 5 PDB
- Residue 30
- the krab-related domain
Similar variants
- PRDM9 c.301+67A>G Benign ★★ same type
- PRDM9 c.509-41C>T Benign ★★ same type
- PRDM9 c.883-52C>T Benign ★★ same type
- PRDM9 c.*125G>A Benign ★★ same type
- PRDM9 c.*37A>G Benign ★★ same type
- PRDM9 p.Asn790His Likely benign ★★ same type
- PRDM9 p.Gly144= Benign ★★ same type
- PRDM9 p.Thr681Ser Benign/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/prdm9-p-asp30 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown