Is BBOF1 p.Lys98Glu (c.292A>G) pathogenic?

BBOF1 p.Lys98Glu (c.292A>G) is classified Uncertain significance in BBOF1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-12). AlphaMissense: likely benign (0.1042); Absent from gnomAD v4.1.

How common is BBOF1 p.Lys98Glu (c.292A>G) in the general population?

BBOF1 p.Lys98Glu (c.292A>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BBOF1 p.Lys98Glu (c.292A>G)?

AlphaMissense predicts likely benign (score 0.1042) — an in-silico prediction, not a clinical call.

BBOF1 p.Lys98Glu

c.292A>G · VCV3260525

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1042 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,556,916)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1042	likely benign
REVEL	0.102	moderately benign-leaning
SaProt	LLR -5.98	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 5.1	GERP 0.47, phastCons 1
Regional constraint	o/e 0.89	unconstrained · MANE · 45 kb · p 0.007 · regional, not allelic
Overall
CADD	18.97	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

No allele count reported in gnomAD v4.1 (AN 1,556,916). 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: BBOF1
Protein: p.Lys98Glu
Coding: c.292A>G
MANE Select: NM_025057
Type: single nucleotide variant
Location: chr14:74029190 (GRCh38)
Gene constraint: LOEUF 1.032 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.40

Full BBOF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ALDH6A1 c.112-11G>T Benign ★★ same type
ALDH6A1 c.731-12T>C Benign/Likely benign ★★ same type
ALDH6A1 c.*494A>T Benign ★★ same type
ALDH6A1 p.Asp137Ala Uncertain significance ★ same type
ALDH6A1 p.Met198Leu Uncertain significance ★ ⚠ same type
ALDH6A1 p.Thr96Ile Uncertain significance ★ ⚠ same type
ALDH6A1 p.Val49Ile Conflicting classifications of pathogenicity ★ ⚠ same type
BBOF1 p.Ala317Thr 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/bbof1-p-lys98glu (accessed [today's date]).

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