Genetic Variant BST2:c.*170A>C (chr19-17403172-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_004335.4(BST2):c.*170A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.95 in 989,458 control chromosomes in the GnomAD database, including 447,040 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 0.91 ( 63820 hom., cov: 30)

Exomes 𝑓: 0.96 ( 383220 hom. )

Consequence

BST2
NM_004335.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.07

Publications

8 publications found

Variant links:

Genes affected

BST2 (HGNC:1119): (bone marrow stromal cell antigen 2) Bone marrow stromal cells are involved in the growth and development of B-cells. The specific function of the protein encoded by the bone marrow stromal cell antigen 2 is undetermined; however, this protein may play a role in pre-B-cell growth and in rheumatoid arthritis. [provided by RefSeq, Jul 2008]

BST2 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=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BST2	NM_004335.4 link	c.*170A>C		3_prime_UTR_variant	Exon 5 of 5	ENST00000252593.7	NP_004326.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
BST2	ENST00000252593.7 link	c.*170A>C	3_prime_UTR_variant	Exon 5 of 5	1	NM_004335.4	ENSP00000252593.6
BST2	ENST00000527220.2 link	n.*343A>C	non_coding_transcript_exon_variant	Exon 4 of 4	2		ENSP00000505650.1
BST2	ENST00000527220.2 link	n.*343A>C	3_prime_UTR_variant	Exon 4 of 4	2		ENSP00000505650.1
BST2	ENST00000533098.5 link	n.*69A>C	downstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.914

AC:

138843

AN:

151924

Hom.:

63772

Cov.:

show subpopulations

Gnomad AFR

AF:

0.867

Gnomad AMI

AF:

0.931

Gnomad AMR

AF:

0.918

Gnomad ASJ

AF:

0.990

Gnomad EAS

AF:

0.620

Gnomad SAS

AF:

0.955

Gnomad FIN

AF:

0.889

Gnomad MID

AF:

0.959

Gnomad NFE

AF:

0.960

Gnomad OTH

AF:

0.939

GnomAD4 exome

AF:

0.956

AC:

800767

AN:

837414

Hom.:

383220

Cov.:

AF XY:

0.957

AC XY:

370488

AN XY:

387194

show subpopulations

African (AFR)

AF:

0.862

AC:

13626

AN:

15806

American (AMR)

AF:

0.925

AC:

1406

AN:

1520

Ashkenazi Jewish (ASJ)

AF:

0.991

AC:

5135

AN:

5184

East Asian (EAS)

AF:

0.602

AC:

2205

AN:

3660

South Asian (SAS)

AF:

0.960

AC:

16501

AN:

17188

European-Finnish (FIN)

AF:

0.910

AC:

322

AN:

354

Middle Eastern (MID)

AF:

0.955

AC:

1556

AN:

1630

European-Non Finnish (NFE)

AF:

0.960

AC:

734116

AN:

764608

Other (OTH)

AF:

0.943

AC:

25900

AN:

27464

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

2337

4675

7012

9350

11687

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

20262

40524

60786

81048

101310

<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:

0.914

AC:

138948

AN:

152044

Hom.:

63820

Cov.:

AF XY:

0.909

AC XY:

67566

AN XY:

74300

show subpopulations

African (AFR)

AF:

0.867

AC:

35934

AN:

41456

American (AMR)

AF:

0.918

AC:

14020

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.990

AC:

3435

AN:

3470

East Asian (EAS)

AF:

0.620

AC:

3192

AN:

5152

South Asian (SAS)

AF:

0.955

AC:

4604

AN:

4820

European-Finnish (FIN)

AF:

0.889

AC:

9407

AN:

10586

Middle Eastern (MID)

AF:

0.959

AC:

282

AN:

294

European-Non Finnish (NFE)

AF:

0.960

AC:

65234

AN:

67972

Other (OTH)

AF:

0.941

AC:

1991

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.517

Heterozygous variant carriers

599

1198

1797

2396

2995

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

902

1804

2706

3608

4510

<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:

0.945

Hom.:

276493

Bravo

AF:

0.911

Asia WGS

AF:

0.822

AC:

2862

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

2.2

(source)

DANN

Benign

0.42

PhyloP100

-1.1

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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