Is BATF3 p.Val16Asp (c.47T>A) pathogenic?

BATF3 p.Val16Asp (c.47T>A) is classified Uncertain significance in BATF3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-31). AlphaMissense: likely benign (0.2828); Absent from gnomAD v4.1.

How common is BATF3 p.Val16Asp (c.47T>A) in the general population?

BATF3 p.Val16Asp (c.47T>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BATF3 p.Val16Asp (c.47T>A)?

AlphaMissense predicts likely benign (score 0.2828) — an in-silico prediction, not a clinical call.

BATF3 p.Val16Asp

c.47T>A · VCV4196929

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2828 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2828	likely benign
REVEL	0.071	moderately benign-leaning
SaProt	LLR -7.71	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.7	GERP -0.8, phastCons 0.62
Regional constraint	o/e 0.83	unconstrained · MANE · 13 kb · p 0.03 · regional, not allelic
Overall
CADD	21.5	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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: BATF3
Protein: p.Val16Asp
Coding: c.47T>A
MANE Select: NM_018664
Type: single nucleotide variant
Location: chr1:212699716 (GRCh38)
Gene constraint: LOEUF 1.094 · pLI 0.06 (gnomAD)
Structure: AlphaFold pLDDT 83.05
Residue 16: the 'disordered' region

Full BATF3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BATF3 p.Ala17Val Uncertain significance ★ ⚠ same type
BATF3 p.Asp119Gly Uncertain significance ★ ⚠ same type
BATF3 p.Asp34Val Uncertain significance ★ ⚠ same type
BATF3 p.Gln72Arg Uncertain significance ★ ⚠ same type
BATF3 p.Gly123Ser Uncertain significance ★ ⚠ same type
BATF3 p.Gly4Arg Uncertain significance ★ ⚠ same type
BATF3 p.Leu5Phe Uncertain significance ★ ⚠ same type
BATF3 p.Lys62Glu 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/batf3-p-val16asp (accessed [today's date]).

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