rs11931532

chr4-15724143-T-C

Variant summary

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

The NM_004334.3(BST1):c.851+1209T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,130 control chromosomes in the GnomAD database, including 2,590 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 0.13 (2590 hom., cov: 32)
• Consequence: BST1 NM_004334.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.47

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=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BST1	NM_004334.3	c.851+1209T>C		intron_variant		ENST00000265016.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BST1	ENST00000265016.9	c.851+1209T>C		intron_variant		1	NM_004334.3	P1
BST1	ENST00000382346.7	c.896+1209T>C		intron_variant		5
BST1	ENST00000514445.5	c.401+1209T>C		intron_variant		3
BST1	ENST00000514989.1	c.274+1209T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20446 AN: 152012 Hom.: 2591 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.0828

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0330

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.135 AC: 20466 AN: 152130 Hom.: 2590 Cov.: 32 AF XY: 0.140 AC XY: 10413 AN XY: 74394

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.0510

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.0828

Gnomad4 NFE AF: 0.0331

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0549 Hom.: 1292

Bravo AF: 0.147

Asia WGS AF: 0.302 AC: 1047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.0050
Dann	Benign	0.19

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs11931532; hg19: chr4-15725766;