Is BSN p.Arg930His (c.2789G>A) pathogenic?

BSN p.Arg930His (c.2789G>A) is classified Uncertain significance in BSN (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-26). AlphaMissense: ambiguous (0.3896); Very rare (popmax 0.00324%, nfe).

How common is BSN p.Arg930His (c.2789G>A) in the general population?

BSN p.Arg930His (c.2789G>A) is very rare (popmax 0.00324%, nfe) (gnomAD).

What do computational predictors say about BSN p.Arg930His (c.2789G>A)?

AlphaMissense predicts ambiguous (score 0.3896) — an in-silico prediction, not a clinical call.

BSN p.Arg930His

c.2789G>A · rs749614597 · VCV2406524

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3896 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00324%, nfe)

Computational evidence

Protein change
AlphaMissense	0.3896	ambiguous
REVEL	0.426	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.6, phastCons 1
Regional constraint	o/e 0.89	unconstrained · MANE · 98 kb · p 3.9e-05 · regional, not allelic
Overall
CADD	29.4	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 0.00324% European (non-Finnish) · 38/1,174,264 alleles

Filtering AF 0.00241% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00211%

Overall 0.00274% 44/1,603,212 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00324%	30,902
Remaining individualsnot grpmax-eligible	0.00323%	30,940
African / African-American	0.00268%	37,287
Admixed American	0.0017%	58,802
South Asian	0.00112%	89,634

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.Arg930His
Coding: c.2789G>A
MANE Select: NM_003458
dbSNP: rs749614597
Type: single nucleotide variant
Location: chr3:49652345 (GRCh38)
Gene constraint: LOEUF 0.271 · pLI 1.00 (gnomAD)

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

Similar variants

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BSN p.Arg1145Trp Uncertain significance ★★ ⚠ same type
BSN p.Arg2221His Uncertain significance ★★ ⚠ same type
BSN p.Arg3229Gln Uncertain significance ★★ same type
BSN p.Arg976His Uncertain significance ★★ same type
BSN p.His1842Arg 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/bsn-p-arg930his (accessed [today's date]).

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