dbSNP rs3213710: BST1:c.612-9G>A (chr4-15715698-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_004334.3(BST1):c.612-9G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 1,557,570 control chromosomes in the GnomAD database, including 207,443 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 0.45 ( 16451 hom., cov: 32)

Exomes 𝑓: 0.52 ( 190992 hom. )

Consequence

BST1
NM_004334.3 intron

Scores

Splicing: ADA: 0.001913

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0270

Publications

34 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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.34).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004334.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BST1	NM_004334.3	MANE Select	c.612-9G>A		intron	N/A	NP_004325.2	Q10588-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BST1	ENST00000265016.9	TSL:1 MANE Select	c.612-9G>A	intron	N/A	ENSP00000265016.4	Q10588-1
BST1	ENST00000382346.7	TSL:5	c.657-9G>A	intron	N/A	ENSP00000371783.3	A6NC48
BST1	ENST00000897441.1		c.612-9G>A	intron	N/A	ENSP00000567500.1

Frequencies

GnomAD3 genomes

AF:

0.447

AC:

67944

AN:

151840

Hom.:

16443

Cov.:

show subpopulations

Gnomad AFR

AF:

0.259

Gnomad AMI

AF:

0.546

Gnomad AMR

AF:

0.520

Gnomad ASJ

AF:

0.466

Gnomad EAS

AF:

0.431

Gnomad SAS

AF:

0.565

Gnomad FIN

AF:

0.561

Gnomad MID

AF:

0.563

Gnomad NFE

AF:

0.517

Gnomad OTH

AF:

0.473

GnomAD2 exomes

AF:

0.518

AC:

118741

AN:

229426

AF XY:

0.523

show subpopulations

Gnomad AFR exome

AF:

0.247

Gnomad AMR exome

AF:

0.628

Gnomad ASJ exome

AF:

0.479

Gnomad EAS exome

AF:

0.437

Gnomad FIN exome

AF:

0.558

Gnomad NFE exome

AF:

0.519

Gnomad OTH exome

AF:

0.520

GnomAD4 exome

AF:

0.518

AC:

727548

AN:

1405612

Hom.:

190992

Cov.:

AF XY:

0.520

AC XY:

363982

AN XY:

699828

show subpopulations

African (AFR)

AF:

0.255

AC:

8018

AN:

31446

American (AMR)

AF:

0.614

AC:

23642

AN:

38512

Ashkenazi Jewish (ASJ)

AF:

0.481

AC:

12151

AN:

25248

East Asian (EAS)

AF:

0.427

AC:

16494

AN:

38624

South Asian (SAS)

AF:

0.583

AC:

46295

AN:

79414

European-Finnish (FIN)

AF:

0.557

AC:

29462

AN:

52882

Middle Eastern (MID)

AF:

0.583

AC:

3268

AN:

5604

European-Non Finnish (NFE)

AF:

0.519

AC:

558561

AN:

1075626

Other (OTH)

AF:

0.509

AC:

29657

AN:

58256

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

15984

31968

47951

63935

79919

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16022

32044

48066

64088

80110

<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:

0.447

AC:

67969

AN:

151958

Hom.:

16451

Cov.:

AF XY:

0.452

AC XY:

33564

AN XY:

74254

show subpopulations

African (AFR)

AF:

0.259

AC:

10716

AN:

41424

American (AMR)

AF:

0.521

AC:

7955

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.466

AC:

1614

AN:

3466

East Asian (EAS)

AF:

0.431

AC:

2229

AN:

5172

South Asian (SAS)

AF:

0.564

AC:

2717

AN:

4814

European-Finnish (FIN)

AF:

0.561

AC:

5918

AN:

10546

Middle Eastern (MID)

AF:

0.568

AC:

167

AN:

294

European-Non Finnish (NFE)

AF:

0.517

AC:

35151

AN:

67952

Other (OTH)

AF:

0.476

AC:

1006

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1810

3621

5431

7242

9052

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

630

1260

1890

2520

3150

<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:

0.507

Hom.:

42838

Bravo

AF:

0.435

Asia WGS

AF:

0.496

AC:

1725

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.34

CADD

Benign

(source)

DANN

Benign

0.79

PhyloP100

-0.027

PromoterAI

-0.0074

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.0019

dbscSNV1_RF

Benign

0.028

SpliceAI score (max)

0.070

Details are displayed if max score is > 0.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over