rs4538475

Positions:

• chr4-15736314-A-G
• chr4-15736314-A-T

Variant summary

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

The ENST00000514445.5(BST1):​c.*12+183A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 151,716 control chromosomes in the GnomAD database, including 4,905 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 0.24 (4905 hom., cov: 30)
• Consequence: BST1 ENST00000514445.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BST1	XM_005248186.3	c.852-1473A>G		intron_variant			XP_005248243.1
BST1	XM_011513878.4	c.851+13380A>G		intron_variant			XP_011512180.1
BST1	XM_011513879.3	c.852-1394A>G		intron_variant			XP_011512181.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BST1	ENST00000514445.5	c.*12+183A>G		intron_variant		3		ENSP00000420925
BST1	ENST00000514989.1	c.275-1473A>G		intron_variant		3		ENSP00000424761

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35964 AN: 151598 Hom.: 4901 Cov.: 30

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.237 AC: 36009 AN: 151716 Hom.: 4905 Cov.: 30 AF XY: 0.242 AC XY: 17928 AN XY: 74168

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.231

Alfa AF: 0.185 Hom.: 6125

Bravo AF: 0.250

Asia WGS AF: 0.360 AC: 1250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4538475; hg19: chr4-15737937;