Is BSN p.Asp1458= (c.4374C>T) pathogenic?

BSN p.Asp1458= (c.4374C>T) is classified Benign in BSN (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-07-30). Low-frequency (popmax 1.4%, eas); Associated with BSN-related disorder.

What condition is associated with BSN p.Asp1458= (c.4374C>T)?

BSN p.Asp1458= (c.4374C>T) is associated with BSN-related disorder (ClinVar).

How common is BSN p.Asp1458= (c.4374C>T) in the general population?

BSN p.Asp1458= (c.4374C>T) is low-frequency (popmax 1.4%, eas) (gnomAD).

BSN p.Asp1458=

c.4374C>T · rs117032536 · VCV3050292

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 1.4%, eas)

Conditions

BSN-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -5.6	GERP -4.5
Overall
CADD	0.345	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.4% East Asian · 630/44,882 alleles

Filtering AF 1.31% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.28%

Overall 0.0503% 812/1,614,142 alleles · low-frequency

Ancestry group	Frequency	1 in
East Asiangrpmax	1.4%	71
South Asian	0.102%	979
Middle Eastern	0.099%	1,010
Remaining individualsnot grpmax-eligible	0.0496%	2,016
African / African-American	0.00533%	18,758
European (non-Finnish)	0.00381%	26,223
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,604
Admixed American	0.00333%	30,009

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.Asp1458=
Coding: c.4374C>T
MANE Select: NM_003458
dbSNP: rs117032536
Type: single nucleotide variant
Location: chr3:49653930 (GRCh38)
Gene constraint: LOEUF 0.271 · pLI 1.00 (gnomAD)
Residue 1458: the 'disordered' region

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-asp1458 (accessed [today's date]).

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