Is PRMT7 p.Asp70= (c.210C>T) pathogenic?

PRMT7 p.Asp70= (c.210C>T) is classified Benign/Likely benign in PRMT7 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-01-05). Ultra-rare (popmax 0.0658%, mid).

How common is PRMT7 p.Asp70= (c.210C>T) in the general population?

PRMT7 p.Asp70= (c.210C>T) is ultra-rare (popmax 0.0658%, mid) (gnomAD).

PRMT7 p.Asp70=

c.210C>T · VCV3712511

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0658%, mid)

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 0.82	GERP 0.42, phastCons 1
Overall
CADD	11.24	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0658% Middle Eastern · 4/6,078 alleles

Filtering AF 0.0224% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0188%

Overall 0.00954% 154/1,613,854 alleles · ultra-rare exomes 140/1,461,584 · genomes 14/152,270 · joint denominator

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.182%	548
Middle Easterngrpmax	0.0658%	1,520
South Asian	0.0308%	3,252
Remaining individualsnot grpmax-eligible	0.0224%	4,463
African / African-American	0.0214%	4,683
European (non-Finnish)	0.00322%	31,052

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Asp70=
Coding: c.210C>T
MANE Select: NM_019023
Type: single nucleotide variant
Location: chr16:68324760 (GRCh38)
Gene constraint: LOEUF 1.01 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.19
Residue 70: the sam-dependent mtase prmt-type 1 domain

Full PRMT7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PRMT7 p.Asp70Asn Uncertain significance ★★ ⚠ same residue
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

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-asp70 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown