Is BMS1 p.Asp505= (c.1515C>T) pathogenic?

BMS1 p.Asp505= (c.1515C>T) is classified Likely benign in BMS1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-11-20). Ultra-rare (popmax 0.0209%, sas); Associated with BMS1-related disorder.

What condition is associated with BMS1 p.Asp505= (c.1515C>T)?

BMS1 p.Asp505= (c.1515C>T) is associated with BMS1-related disorder (ClinVar).

How common is BMS1 p.Asp505= (c.1515C>T) in the general population?

BMS1 p.Asp505= (c.1515C>T) is ultra-rare (popmax 0.0209%, sas) (gnomAD).

BMS1 p.Asp505=

c.1515C>T · rs751387779 · VCV3048898

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0209%, sas)

Conditions

BMS1-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 -5.1	GERP -3.1
Overall
CADD	1.597	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0209% South Asian · 19/91,076 alleles

Filtering AF 0.0136% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0114%

Overall 0.0026% 38/1,461,880 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0209%	4,793
European (non-Finnish)	0.00161%	62,106

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: BMS1
Protein: p.Asp505=
Coding: c.1515C>T
MANE Select: NM_014753
dbSNP: rs751387779
Type: single nucleotide variant
Location: chr10:42796759 (GRCh38)
Gene constraint: LOEUF 0.507 · pLI 0.50 (gnomAD)
Structure: AlphaFold pLDDT 72.04 · 3 PDB
Residue 505: the 'disordered' region

Full BMS1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

BMS1-related disorder

Similar variants

BMS1 c.779+7T>A Likely benign same condition
BMS1 c.779+8A>G Likely benign same condition
BMS1 p.Ala549Thr Benign same condition
BMS1 p.Ala864Thr Benign same condition
BMS1 p.Gln419Glu Benign same condition
BMS1 p.Lys399= Benign same condition
BMS1 p.Phe1047Leu Benign same condition
BMS1 p.Thr583= Benign 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/bms1-p-asp505 (accessed [today's date]).

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