Is BSDC1 p.Cys151Phe (c.452G>T) pathogenic?

BSDC1 p.Cys151Phe (c.452G>T) is classified Uncertain significance in BSDC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-07). AlphaMissense: likely benign (0.1023); No allele count reported in gnomAD v4.1 (AN 1,549,324).

How common is BSDC1 p.Cys151Phe (c.452G>T) in the general population?

BSDC1 p.Cys151Phe (c.452G>T) is no allele count reported in gnomAD v4.1 (AN 1,549,324) (gnomAD).

What do computational predictors say about BSDC1 p.Cys151Phe (c.452G>T)?

AlphaMissense predicts likely benign (score 0.1023) — an in-silico prediction, not a clinical call.

BSDC1 p.Cys151Phe

c.452G>T · rs867745719 · VCV2322572

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1023 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,549,324)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1023	likely benign
REVEL	0.117	moderately benign-leaning
SaProt	LLR -9.80	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 2.7	GERP 2.7, phastCons 1
Regional constraint	o/e 0.87	unconstrained · MANE · 28 kb · p 0.0023 · regional, not allelic
Overall
CADD	24.3	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 1,549,324). 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: BSDC1
Protein: p.Cys151Phe
Coding: c.452G>T
MANE Select: NM_018045
dbSNP: rs867745719
Type: single nucleotide variant
Location: chr1:32378800 (GRCh38)
Gene constraint: LOEUF 0.763 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 62.91
Residue 151: the bsd domain

Full BSDC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BSDC1 c.190-36C>G Uncertain significance ★ same type
BSDC1 p.Ala145Thr Uncertain significance ★ ⚠ same type
BSDC1 p.Ala145Val Uncertain significance ★ ⚠ same type
BSDC1 p.Ala20Thr Uncertain significance ★ ⚠ same type
BSDC1 p.Ala28Thr Uncertain significance ★ ⚠ same type
BSDC1 p.Ala295Val Uncertain significance ★ ⚠ same type
BSDC1 p.Ala2Val Uncertain significance ★ ⚠ same type
BSDC1 p.Ala411Val 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/bsdc1-p-cys151phe (accessed [today's date]).

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