Is BRAF p.Phe548= (c.1644T>C) pathogenic?

BRAF p.Phe548= (c.1644T>C) is classified Likely benign in BRAF (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-28). Absent from gnomAD v4.1; Associated with Cardiovascular phenotype.

What condition is associated with BRAF p.Phe548= (c.1644T>C)?

BRAF p.Phe548= (c.1644T>C) is associated with Cardiovascular phenotype (ClinVar).

How common is BRAF p.Phe548= (c.1644T>C) in the general population?

BRAF p.Phe548= (c.1644T>C) is absent from gnomAD v4.1 (gnomAD).

BRAF p.Phe548=

c.1644T>C · VCV3481739

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.185	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.39	GERP -3.1, phastCons 0.64
Overall
CADD	6.955	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: BRAF
Protein: p.Phe548=
Coding: c.1644T>C
MANE Select: NM_004333
Type: single nucleotide variant
Location: chr7:140776962 (GRCh38)
Gene constraint: LOEUF 0.237 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 67.87 · 135 PDB
Residue 548: an α-helix; the protein kinase domain

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

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BRAF p.Phe548Leu Uncertain significance ★ ⚠ same residue
BRAF p.Phe548Ser Uncertain significance ★ ⚠ same residue
BRAF p.Asn236Lys Likely pathogenic ★★ same condition
BRAF p.Gln262Arg Pathogenic/Likely pathogenic ★★ same condition
BRAF p.Glu501Lys Pathogenic/Likely pathogenic ★★ same condition
BRAF c.2127+4A>G Uncertain significance ★★ same condition
BRAF p.Ala27Gly Uncertain significance ★★ ⚠ same condition
BRAF p.Ala42Ser Uncertain significance ★★ ⚠ same condition

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/braf-p-phe548 (accessed [today's date]).

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