Is EAF2 p.Asn232= (c.696T>C) pathogenic?

EAF2 p.Asn232= (c.696T>C) is classified Benign in EAF2 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-07-17). Ultra-rare (popmax 0.0476%, nfe).

How common is EAF2 p.Asn232= (c.696T>C) in the general population?

EAF2 p.Asn232= (c.696T>C) is ultra-rare (popmax 0.0476%, nfe) (gnomAD).

EAF2 p.Asn232=

c.696T>C · rs148765156 · VCV752374

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0476%, nfe)

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 -0.11	GERP -3.6, phastCons 0.13
Overall
CADD	0.547	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0476% European (non-Finnish) · 561/1,178,960 alleles

Filtering AF 0.0443% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.043%

Overall 0.0522% 842/1,612,290 alleles · ultra-rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.461%	217
Finnishnot grpmax-eligible	0.0923%	1,084
Remaining individualsnot grpmax-eligible	0.0849%	1,178
European (non-Finnish)grpmax	0.0476%	2,102
South Asian	0.0209%	4,787
Middle Eastern	0.0165%	6,076
African / African-American	0.016%	6,238
Admixed American	0.00167%	59,874

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: EAF2
Protein: p.Asn232=
Coding: c.696T>C
MANE Select: NM_019100 · reported on NM_018456
dbSNP: rs148765156
Type: single nucleotide variant
Location: chr3:121872748 (GRCh38)
Structure: AlphaFold pLDDT 75.46 · 18 PDB
Residue 232: an α-helix

Full EAF2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DMAP1 p.Arg232His Uncertain significance ★ ⚠ same residue
DMAP1 p.Arg224Ter Uncertain significance ★★ same type
DMAP1 p.Arg283His Uncertain significance ★★ ⚠ same type
DMAP1 p.Tyr196Ser Uncertain significance ★★ ⚠ same type
DMAP1 p.Arg226Trp Likely pathogenic ★ same type
DMAP1 c.1344+3A>G Uncertain significance ★ same type
DMAP1 c.394-1G>C Uncertain significance ★ same type
DMAP1 p.Ala207Thr 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/eaf2-p-asn232 (accessed [today's date]).

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