rs12502586

Variant names:

• chr4-15724941-G-A
• rs12502586
• NM_004334.3:c.851+2007G>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.851+2007G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0696 in 152,210 control chromosomes in the GnomAD database, including 503 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 0.070 (503 hom., cov: 32)
• Consequence: BST1 NM_004334.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.268
• Publications: 11 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BST1	NM_004334.3	c.851+2007G>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.851+2007G>A		intron_variant	Intron 8 of 8	1	NM_004334.3	ENSP00000265016.4

Frequencies

GnomAD3 genomes AF: 0.0696 AC: 10588 AN: 152092 Hom.: 502 Cov.: 32

Gnomad AFR AF: 0.0185

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.0851

Gnomad ASJ AF: 0.0804

Gnomad EAS AF: 0.00251

Gnomad SAS AF: 0.0924

Gnomad FIN AF: 0.0761

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0980

Gnomad OTH AF: 0.0721

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

GnomAD4 genome AF: 0.0696 AC: 10596 AN: 152210 Hom.: 503 Cov.: 32 AF XY: 0.0687 AC XY: 5114 AN XY: 74394

African (AFR) AF: 0.0185 AC: 768 AN: 41562

American (AMR) AF: 0.0855 AC: 1306 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0804 AC: 279 AN: 3470

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5170

South Asian (SAS) AF: 0.0923 AC: 445 AN: 4822

European-Finnish (FIN) AF: 0.0761 AC: 806 AN: 10590

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0980 AC: 6668 AN: 68010

Other (OTH) AF: 0.0704 AC: 149 AN: 2116

Alfa AF: 0.0810 Hom.: 677

Bravo AF: 0.0660

Asia WGS AF: 0.0420 AC: 145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.7
DANN	Benign	0.69
PhyloP100		-0.27
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.14		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: rs12502586; hg19: chr4-15726564;