Is BRAF p.Ala31= (c.93C>A) pathogenic?

BRAF p.Ala31= (c.93C>A) is classified Likely benign in BRAF (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-02-27). Absent from gnomAD v4.1; Associated with RASopathy.

What condition is associated with BRAF p.Ala31= (c.93C>A)?

BRAF p.Ala31= (c.93C>A) is associated with RASopathy (ClinVar).

How common is BRAF p.Ala31= (c.93C>A) in the general population?

BRAF p.Ala31= (c.93C>A) is absent from gnomAD v4.1 (gnomAD).

BRAF p.Ala31=

c.93C>A · rs2129153244 · VCV1766813

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,527,500)

Conditions

RASopathy

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 2.5	GERP 0.67, phastCons 1
Overall
CADD	12.04	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,527,500). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: BRAF
Protein: p.Ala31=
Coding: c.93C>A
MANE Select: NM_004333
dbSNP: rs2129153244
Type: single nucleotide variant
Location: chr7:140924611 (GRCh38)
Gene constraint: LOEUF 0.237 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 67.87 · 135 PDB
Residue 31: the 'disordered' region

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

Disease context

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

Similar variants

BRAF p.Ala31Gly Likely benign ★★★ ⚠ same residue
BRAF p.Ala31Val Uncertain significance ★ ⚠ same residue
BRAF p.Ala31Thr Uncertain significance ★ ⚠ same residue
BRAF p.Ala246Pro Pathogenic ★★★ same condition
BRAF p.Asn581Asp Pathogenic ★★★ same condition
BRAF p.Asp594Val Pathogenic ★★★ same condition
BRAF p.Cys532Tyr Likely pathogenic ★★★ same condition
BRAF p.Gln257Arg Pathogenic ★★★ 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-ala31 (accessed [today's date]).

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