Is ILF3 p.Arg655= (c.1965A>G) pathogenic?

ILF3 p.Arg655= (c.1965A>G) is classified Benign in ILF3 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-05-12). Low-frequency (popmax 1.24%, nfe).

How common is ILF3 p.Arg655= (c.1965A>G) in the general population?

ILF3 p.Arg655= (c.1965A>G) is low-frequency (popmax 1.24%, nfe) (gnomAD).

ILF3 p.Arg655=

c.1965A>G · rs139961882 · VCV781442

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.24%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 4.6	GERP -1.6, phastCons 1
Overall
CADD	10.82	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.24% European (non-Finnish) · 14,622/1,179,308 alleles

Filtering AF 1.22% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.22%

Overall 1.08% 17,479/1,612,346 alleles · low-frequency exomes 16,244/1,460,074 · genomes 1,235/152,272 · joint denominator

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	2.15%	46
European (non-Finnish)grpmax	1.24%	81
Remaining individualsnot grpmax-eligible	0.83%	120
Amishnot grpmax-eligible	0.658%	152
South Asian	0.6%	167
Ashkenazi Jewishnot grpmax-eligible	0.394%	254
Admixed American	0.225%	445
Middle Eastern	0.215%	464
African / African-American	0.2%	500
East Asian	0.00223%	44,848

Finnish 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: ILF3
Protein: p.Arg655=
Coding: c.1965A>G
MANE Select: NM_017620
dbSNP: rs139961882
Type: single nucleotide variant
Location: chr19:10683737 (GRCh38)
Gene constraint: LOEUF 0.309 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 67.74 · 4 PDB
Residue 655: the 'interaction with prmt1' region; the 'disordered' region

Full ILF3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ILF3 p.Ala123Thr Uncertain significance ★ ⚠ same type
ILF3 p.Ala268Val Uncertain significance ★ ⚠ same type
ILF3 p.Ala397Ser Uncertain significance ★ ⚠ same type
ILF3 p.Ala488Thr Uncertain significance ★ ⚠ same type
ILF3 p.Ala494Val Uncertain significance ★ ⚠ same type
ILF3 p.Ala507Val Uncertain significance ★ ⚠ same type
ILF3 p.Ala515Val Uncertain significance ★ ⚠ same type
ILF3 p.Ala573Thr 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/ilf3-p-arg655 (accessed [today's date]).

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