PRMT7 p.Phe652del
c.1951TTC[1] · rs562766169 · VCV712115
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.249%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 2.6, phastCons 1 |
| Overall | ||
| CADD | 15.45 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.249%
Admixed American · 149/59,896 alleles
Filtering AF
0.216%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.204%
Overall
0.118%
1,897/1,613,212 alleles · rare
exomes 1,774/1,460,890 · genomes 123/152,322 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.249% | 402 |
| European (non-Finnish) | 0.141% | 708 |
| Remaining individualsnot grpmax-eligible | 0.0896% | 1,115 |
| African / African-American | 0.028% | 3,572 |
| Finnishnot grpmax-eligible | 0.00314% | 31,868 |
| South Asian | 0.0022% | 45,507 |
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
- PRMT7
- Protein
- p.Phe652del
- Coding
- c.1951TTC[1]
- MANE Select
- NM_019023
- dbSNP
- rs562766169
- Type
- Microsatellite
- Location
- chr16:68357095 (GRCh38)
- Gene constraint
- LOEUF 1.01 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.19
- Residue 652
- the sam-dependent mtase prmt-type 2 domain
Similar variants
- PRMT7 p.Arg358fs Likely pathogenic ★ same type
- PRMT7 p.Glu144fs Pathogenic ★ same type
- PRMT7 p.Leu475fs Likely pathogenic ★ same type
- PRMT7 p.Gly76_Leu77insThrGly Uncertain significance ★ same type
- PRMT7 p.Leu476del Uncertain significance ★ same type
- PRMT7 c.132+22_132+24del Benign ★ same type
- PRMT7 c.1323+12TTG[2] Benign ★ same type
- PRMT7 c.1909-9_1909-7del 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/prmt7-p-phe652del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown