Is BBOF1 p.Asp17Val (c.50A>T) pathogenic?

BBOF1 p.Asp17Val (c.50A>T) is classified Uncertain significance in BBOF1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-13). AlphaMissense: likely benign (0.0907); Very rare (popmax 0.00227%, eas).

How common is BBOF1 p.Asp17Val (c.50A>T) in the general population?

BBOF1 p.Asp17Val (c.50A>T) is very rare (popmax 0.00227%, eas) (gnomAD).

What do computational predictors say about BBOF1 p.Asp17Val (c.50A>T)?

AlphaMissense predicts likely benign (score 0.0907) — an in-silico prediction, not a clinical call.

BBOF1 p.Asp17Val

c.50A>T · rs759708180 · VCV2289576

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0907 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00227%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0907	likely benign
REVEL	0.04	moderately benign-leaning
SaProt	LLR -6.93	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 2.4	GERP -4, phastCons 0.24
Regional constraint	o/e 0.89	unconstrained · MANE · 45 kb · p 0.007 · regional, not allelic
Overall
CADD	17.37	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

Grpmax group 0.00227% East Asian · 1/44,008 alleles

Overall 6.91e-05% 1/1,446,830 alleles · very rare

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: BBOF1
Protein: p.Asp17Val
Coding: c.50A>T
MANE Select: NM_025057
dbSNP: rs759708180
Type: single nucleotide variant
Location: chr14:74019528 (GRCh38)
Gene constraint: LOEUF 1.032 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.40
Residue 17: the 'disordered' region

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-asp17val (accessed [today's date]).

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