4-15724143-T-C

Variant names:

• chr4-15724143-T-C
• rs11931532
• NM_004334.3:c.851+1209T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 25 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=-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 rank	MANE	Protein	UniProt
BST1	NM_004334.3	c.851+1209T>C		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.851+1209T>C		intron_variant	Intron 8 of 8	1	NM_004334.3	ENSP00000265016.4

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

African (AFR) AF: 0.275 AC: 11418 AN: 41458

American (AMR) AF: 0.126 AC: 1929 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0510 AC: 177 AN: 3472

East Asian (EAS) AF: 0.524 AC: 2696 AN: 5146

South Asian (SAS) AF: 0.173 AC: 836 AN: 4824

European-Finnish (FIN) AF: 0.0828 AC: 879 AN: 10610

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0331 AC: 2250 AN: 68010

Other (OTH) AF: 0.120 AC: 253 AN: 2110

Alfa AF: 0.0682 Hom.: 4187

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
PhyloP100		-5.5
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: rs11931532; hg19: chr4-15725766;