Is BSN p.Gly1683= (c.5049C>T) pathogenic?

BSN p.Gly1683= (c.5049C>T) is classified Benign in BSN (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-06-19). Rare (popmax 0.779%, sas); Associated with BSN-related disorder.

What condition is associated with BSN p.Gly1683= (c.5049C>T)?

BSN p.Gly1683= (c.5049C>T) is associated with BSN-related disorder (ClinVar).

How common is BSN p.Gly1683= (c.5049C>T) in the general population?

BSN p.Gly1683= (c.5049C>T) is rare (popmax 0.779%, sas) (gnomAD).

BSN p.Gly1683=

c.5049C>T · rs560401884 · VCV3042729

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.779%, sas)

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 0.009	GERP -4.5, phastCons 0.82
Overall
CADD	4.645	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.779% South Asian · 709/91,028 alleles

Filtering AF 0.731% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.712%

Overall 0.0462% 746/1,613,668 alleles · rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.779%	128
Remaining individualsnot grpmax-eligible	0.048%	2,083
African / African-American	0.004%	25,018
European (non-Finnish)	0.000339%	294,944

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.Gly1683=
Coding: c.5049C>T
MANE Select: NM_003458
dbSNP: rs560401884
Type: single nucleotide variant
Location: chr3:49654605 (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-gly1683 (accessed [today's date]).

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