rs4698412

Positions:

• chr4-15735725-G-A
• chr4-15735725-G-T

Variant summary

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

The ENST00000514445.5(BST1):​c.402-328G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 152,084 control chromosomes in the GnomAD database, including 16,638 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 0.43 (16638 hom., cov: 32)
• Consequence: BST1 ENST00000514445.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BST1	XM_005248186.3	c.852-2062G>A		intron_variant			XP_005248243.1
BST1	XM_011513878.4	c.851+12791G>A		intron_variant			XP_011512180.1
BST1	XM_011513879.3	c.852-1983G>A		intron_variant			XP_011512181.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BST1	ENST00000514445.5	c.402-328G>A		intron_variant		3		ENSP00000420925
BST1	ENST00000514989.1	c.275-2062G>A		intron_variant		3		ENSP00000424761

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66041 AN: 151966 Hom.: 16635 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.434 AC: 66054 AN: 152084 Hom.: 16638 Cov.: 32 AF XY: 0.440 AC XY: 32673 AN XY: 74316

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.581

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.545

Gnomad4 OTH AF: 0.469

Alfa AF: 0.526 Hom.: 47868

Bravo AF: 0.414

Asia WGS AF: 0.477 AC: 1660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4698412; hg19: chr4-15737348;