rs12645693

Variant names:

• chr4-15727911-G-A
• rs12645693
• NM_004334.3:c.852-3829G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
BST1	NM_004334.3	c.852-3829G>A		intron_variant	Intron 8 of 8	ENST00000265016.9	NP_004325.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BST1	ENST00000265016.9	c.852-3829G>A		intron_variant	Intron 8 of 8	1	NM_004334.3	ENSP00000265016.4

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

African (AFR) AF: 0.109 AC: 4504 AN: 41186

American (AMR) AF: 0.109 AC: 1659 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.0502 AC: 174 AN: 3466

East Asian (EAS) AF: 0.525 AC: 2661 AN: 5068

South Asian (SAS) AF: 0.171 AC: 817 AN: 4778

European-Finnish (FIN) AF: 0.0823 AC: 857 AN: 10412

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0325 AC: 2209 AN: 67918

Other (OTH) AF: 0.0839 AC: 176 AN: 2098

Alfa AF: 0.0526 Hom.: 319

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
PhyloP100		0.26
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12645693; hg19: chr4-15729534;