Is BSN p.Pro2484Thr (c.7450C>A) pathogenic?

BSN p.Pro2484Thr (c.7450C>A) is classified Benign in BSN (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-06-27). AlphaMissense: likely benign (0.0644); Low-frequency (popmax 1.2%, sas); Associated with BSN-related disorder.

What condition is associated with BSN p.Pro2484Thr (c.7450C>A)?

BSN p.Pro2484Thr (c.7450C>A) is associated with BSN-related disorder (ClinVar).

How common is BSN p.Pro2484Thr (c.7450C>A) in the general population?

BSN p.Pro2484Thr (c.7450C>A) is low-frequency (popmax 1.2%, sas) (gnomAD).

What do computational predictors say about BSN p.Pro2484Thr (c.7450C>A)?

AlphaMissense predicts likely benign (score 0.0644) — an in-silico prediction, not a clinical call.

BSN p.Pro2484Thr

c.7450C>A · rs199514462 · VCV3042685

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0644 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.2%, sas)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Conditions

BSN-related disorder

Computational evidence

Protein change
AlphaMissense	0.0644	likely benign
REVEL	0.033	moderately benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.51	GERP 0.43, phastCons 0.039
Regional constraint	o/e 0.88	unconstrained · MANE · 12 kb · p 3.9e-13 · regional, not allelic
Overall
CADD	9.502	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.2% South Asian · 1,096/90,982 alleles

Filtering AF 1.15% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.12%

Overall 0.0721% 1,161/1,610,354 alleles · low-frequency

Ancestry group	Frequency	1 in
South Asiangrpmax	1.2%	83
Remaining individualsnot grpmax-eligible	0.0851%	1,176
Middle Eastern	0.0165%	6,056
African / African-American	0.004%	25,005
Admixed American	0.00167%	59,930
European (non-Finnish)	0.000594%	168,253

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: BSN
Protein: p.Pro2484Thr
Coding: c.7450C>A
MANE Select: NM_003458
dbSNP: rs199514462
Type: single nucleotide variant
Location: chr3:49657006 (GRCh38)
Gene constraint: LOEUF 0.271 · pLI 1.00 (gnomAD)

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

Disease context

BSN-related disorder

Similar variants

BSN p.Arg1145Trp Uncertain significance ★★ ⚠ same condition
BSN p.Leu2466Ile Uncertain significance ★★ ⚠ same condition
BSN p.Pro2732Arg Uncertain significance ★★ same condition
BSN p.Gln1776Ter Likely pathogenic ★ same condition
BSN p.Gln3155Ter Likely pathogenic ★ same condition
BSN p.Gln875Ter Pathogenic ★ same condition
BSN p.Arg1066Cys Uncertain significance ★ ⚠ same condition
BSN p.Arg110Ter Uncertain significance ★ 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/bsn-p-pro2484thr (accessed [today's date]).

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