dbSNP rs12646913: BST1:c.*13-134A>G (chr4-15737653-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000514445.5(BST1):c.*13-134A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0795 in 475,442 control chromosomes in the GnomAD database, including 1,860 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 0.098 ( 910 hom., cov: 32)

Exomes 𝑓: 0.071 ( 950 hom. )

Consequence

BST1
ENST00000514445.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.11

Publications

6 publications found

Variant links:

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]

BST1 links:

ENSG00000294363 (HGNC:58739):

ENSG00000294363 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
BST1	XM_017008565.3 link	c.*13-134A>G	intron_variant	Intron 9 of 9	XP_016864054.1
BST1	XM_011513878.4 link	c.851+14719A>G	intron_variant	Intron 8 of 8	XP_011512180.1
BST1	XM_017008566.3 link	c.851+14719A>G	intron_variant	Intron 8 of 8	XP_016864055.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
BST1	ENST00000514445.5 link	c.*13-134A>G	intron_variant	Intron 6 of 6	3	ENSP00000420925.1	H0Y8G4
BST1	ENST00000514989.1 link	c.273-134A>G	intron_variant	Intron 4 of 4	3	ENSP00000424761.1	H0Y9Q9
ENSG00000294363	ENST00000723151.1 link	n.187-3339T>C	intron_variant	Intron 2 of 2
BST1	ENST00000850863.1 link	n.851+14719A>G	intron_variant	Intron 8 of 9		ENSP00000520950.1

Frequencies

GnomAD3 genomes

AF:

0.0981

AC:

14859

AN:

151504

Hom.:

902

Cov.:

show subpopulations

Gnomad AFR

AF:

0.156

Gnomad AMI

AF:

0.120

Gnomad AMR

AF:

0.0962

Gnomad ASJ

AF:

0.165

Gnomad EAS

AF:

0.0523

Gnomad SAS

AF:

0.0558

Gnomad FIN

AF:

0.0249

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.0774

Gnomad OTH

AF:

0.112

GnomAD4 exome

AF:

0.0707

AC:

22890

AN:

323830

Hom.:

950

AF XY:

0.0699

AC XY:

12441

AN XY:

177948

show subpopulations

African (AFR)

AF:

0.147

AC:

1116

AN:

7578

American (AMR)

AF:

0.0560

AC:

1261

AN:

22504

Ashkenazi Jewish (ASJ)

AF:

0.149

AC:

1236

AN:

8316

East Asian (EAS)

AF:

0.0561

AC:

502

AN:

8954

South Asian (SAS)

AF:

0.0563

AC:

3061

AN:

54410

European-Finnish (FIN)

AF:

0.0325

AC:

360

AN:

11072

Middle Eastern (MID)

AF:

0.151

AC:

408

AN:

2694

European-Non Finnish (NFE)

AF:

0.0706

AC:

13711

AN:

194170

Other (OTH)

AF:

0.0874

AC:

1235

AN:

14132

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

895

1791

2686

3582

4477

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

246

492

738

984

1230

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0982

AC:

14894

AN:

151612

Hom.:

910

Cov.:

AF XY:

0.0945

AC XY:

7009

AN XY:

74170

show subpopulations

African (AFR)

AF:

0.157

AC:

6404

AN:

40894

American (AMR)

AF:

0.0960

AC:

1466

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.165

AC:

572

AN:

3470

East Asian (EAS)

AF:

0.0521

AC:

270

AN:

5186

South Asian (SAS)

AF:

0.0556

AC:

269

AN:

4834

European-Finnish (FIN)

AF:

0.0249

AC:

265

AN:

10624

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0774

AC:

5264

AN:

68024

Other (OTH)

AF:

0.113

AC:

238

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

668

1336

2005

2673

3341

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

158

316

474

632

790

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0847

Hom.:

331

Bravo

AF:

0.107

Asia WGS

AF:

0.0580

AC:

203

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

5.7

(source)

DANN

Benign

0.69

PhyloP100

1.1

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over