rs12645693

chr4-15727911-G-A

Variant summary

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

The NM_004334.3(BST1):c.852-3829G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0864 in 151,318 control chromosomes in the GnomAD database, including 1,188 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 0.086 (1188 hom., cov: 30)
• Consequence: BST1 NM_004334.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.263

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BST1	NM_004334.3	c.852-3829G>A		intron_variant		ENST00000265016.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BST1	ENST00000265016.9	c.852-3829G>A		intron_variant		1	NM_004334.3	P1
BST1	ENST00000382346.7	c.897-3829G>A		intron_variant		5
BST1	ENST00000514445.5	c.401+4977G>A		intron_variant		3
BST1	ENST00000514989.1	c.274+4977G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0864 AC: 13069 AN: 151200 Hom.: 1189 Cov.: 30

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0502

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.0823

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0325

Gnomad OTH AF: 0.0843

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

GnomAD4 genome AF: 0.0864 AC: 13077 AN: 151318 Hom.: 1188 Cov.: 30 AF XY: 0.0925 AC XY: 6836 AN XY: 73908

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.0502

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.0823

Gnomad4 NFE AF: 0.0325

Gnomad4 OTH AF: 0.0839

Alfa AF: 0.0532 Hom.: 277

Bravo AF: 0.0931

Asia WGS AF: 0.293 AC: 1018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	7.1
Dann	Benign	0.64

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: rs12645693; hg19: chr4-15729534;