rs10018756

chr4-15722169-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004334.3(BST1):c.792-706A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 152,156 control chromosomes in the GnomAD database, including 5,499 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.26 (5499 hom., cov: 32)
• Consequence: BST1 NM_004334.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661

Genes affected

BST1 (HGNC:1118): (bone marrow stromal cell antigen 1) Bone marrow stromal cell antigen-1 is a stromal cell line-derived glycosylphosphatidylinositol-anchored molecule that facilitates pre-B-cell growth. The deduced amino acid sequence exhibits 33% similarity with CD38. BST1 expression is enhanced in bone marrow stromal cell lines derived from patients with rheumatoid arthritis. The polyclonal B-cell abnormalities in rheumatoid arthritis may be, at least in part, attributed to BST1 overexpression in the stromal cell population. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BST1	NM_004334.3	c.792-706A>T		intron_variant		ENST00000265016.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BST1	ENST00000265016.9	c.792-706A>T		intron_variant		1	NM_004334.3	P1

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40109 AN: 152038 Hom.: 5472 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.265

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.264 AC: 40182 AN: 152156 Hom.: 5499 Cov.: 32 AF XY: 0.263 AC XY: 19535 AN XY: 74400

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.265

Alfa AF: 0.241 Hom.: 583

Bravo AF: 0.275

Asia WGS AF: 0.243 AC: 847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.1
Dann	Benign	0.49

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10018756; hg19: chr4-15723792;