Is BRF1 p.Gln560= (c.1680G>A) pathogenic?

BRF1 p.Gln560= (c.1680G>A) is classified Likely benign in BRF1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-01). Absent from gnomAD v4.1.

How common is BRF1 p.Gln560= (c.1680G>A) in the general population?

BRF1 p.Gln560= (c.1680G>A) is absent from gnomAD v4.1 (gnomAD).

BRF1 p.Gln560=

c.1680G>A · VCV3898583

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 -0.56	GERP -2
Overall
CADD	0.994	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: BRF1
Protein: p.Gln560=
Coding: c.1680G>A
MANE Select: NM_004926 · reported on NM_001519
Type: single nucleotide variant
Location: chr14:105217636 (GRCh38)
Structure: AlphaFold pLDDT 59.70 · 2 PDB

Full BRF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BRF1 p.Gln560Arg Likely benign ★ same residue
BRF1 p.Pro292His Pathogenic/Likely pathogenic ★★ same type
BRF1 p.Ser226Leu Pathogenic/Likely pathogenic ★★ same type
BRF1 p.Ala565Ser Uncertain significance ★★ ⚠ same type
BRF1 p.Arg213Lys Uncertain significance ★★ ⚠ same type
BRF1 p.Arg216Gln Uncertain significance ★★ ⚠ same type
BRF1 p.Arg261Gln Uncertain significance ★★ ⚠ same type
BRF1 p.Arg302Trp 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/brf1-p-gln560 (accessed [today's date]).

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