PRMT7 p.Ala648=
c.1944C>T · rs768884535 · VCV2646662
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0099%, 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 -13 | GERP -5.2 |
| Overall | ||
| CADD | 0.517 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0099%
South Asian · 9/90,944 alleles
Filtering AF
0.00514%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00376%
Overall
0.0036%
58/1,612,586 alleles · very rare
exomes 48/1,460,386 · genomes 10/152,200 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0099% | 10,105 |
| Admixed American | 0.00836% | 11,957 |
| European (non-Finnish) | 0.00348% | 28,767 |
| East Asian | 0.00223% | 44,894 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,436 |
| African / African-American | 0.00134% | 74,890 |
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.Ala648=
- Coding
- c.1944C>T
- MANE Select
- NM_019023
- dbSNP
- rs768884535
- Type
- single nucleotide variant
- Location
- chr16:68357089 (GRCh38)
- Gene constraint
- LOEUF 1.01 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.19
- Residue 648
- the sam-dependent mtase prmt-type 2 domain
Similar variants
- PRMT7 c.1056-1G>T Pathogenic/Likely pathogenic ★★ same type
- PRMT7 p.Arg274Ter Pathogenic/Likely pathogenic ★★ same type
- PRMT7 p.Arg390Ter Pathogenic ★★ same type
- PRMT7 p.Cys571Ter Pathogenic ★★ same type
- PRMT7 p.Gln323Ter Pathogenic ★★ same type
- PRMT7 p.Glu108Ter Pathogenic/Likely pathogenic ★★ same type
- PRMT7 p.Tyr159Ter Pathogenic ★★ same type
- PRMT7 p.Ala162Thr 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/prmt7-p-ala648 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown