Genetic Variant BDKRB2:c.*382T>C (chr14-96241886-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001379692.1(BDKRB2):c.*382T>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 0.0796 in 178,836 control chromosomes in the GnomAD database, including 707 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 0.079 ( 595 hom., cov: 33)

Exomes 𝑓: 0.085 ( 112 hom. )

Consequence

BDKRB2
NM_001379692.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.22

Publications

16 publications found

Variant links:

Genes affected

BDKRB2 (HGNC:1030): (bradykinin receptor B2) This gene encodes a receptor for bradykinin. The 9 aa bradykinin peptide elicits many responses including vasodilation, edema, smooth muscle spasm and pain fiber stimulation. Bradykinin is released upon activation by pathophysiologic conditions such as trauma and inflammation, and binds to its kinin receptors, B1 and B2. The B2 receptor associates with G proteins that stimulate a phosphatidylinositol-calcium second messenger system. [provided by RefSeq, Apr 2020]

BDKRB2 links:

ENSG00000258691 (HGNC:):

ENSG00000258691 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=-0.93).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BDKRB2	NM_001379692.1 link	c.*382T>C		3_prime_UTR_variant	Exon 3 of 3	ENST00000554311.2	NP_001366621.1
BDKRB2	NM_000623.4 link	c.*382T>C		3_prime_UTR_variant	Exon 3 of 3		NP_000614.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
BDKRB2	ENST00000554311.2 link	c.*382T>C	3_prime_UTR_variant	Exon 3 of 3	1	NM_001379692.1	ENSP00000450482.1
BDKRB2	ENST00000542454.2 link	c.*382T>C	3_prime_UTR_variant	Exon 3 of 3	1		ENSP00000439459.2
ENSG00000258691	ENST00000553811.1 link	c.74+4705T>C	intron_variant	Intron 2 of 3	2		ENSP00000450984.1

Frequencies

GnomAD3 genomes

AF:

0.0786

AC:

11960

AN:

152136

Hom.:

593

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0467

Gnomad AMI

AF:

0.103

Gnomad AMR

AF:

0.0441

Gnomad ASJ

AF:

0.110

Gnomad EAS

AF:

0.00193

Gnomad SAS

AF:

0.0568

Gnomad FIN

AF:

0.107

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.108

Gnomad OTH

AF:

0.0469

GnomAD4 exome

AF:

0.0855

AC:

2272

AN:

26582

Hom.:

112

Cov.:

AF XY:

0.0802

AC XY:

1070

AN XY:

13338

show subpopulations

African (AFR)

AF:

0.0388

AC:

AN:

954

American (AMR)

AF:

0.0290

AC:

AN:

2244

Ashkenazi Jewish (ASJ)

AF:

0.127

AC:

118

AN:

930

East Asian (EAS)

AF:

0.000678

AC:

AN:

1476

South Asian (SAS)

AF:

0.0363

AC:

AN:

744

European-Finnish (FIN)

AF:

0.108

AC:

123

AN:

1136

Middle Eastern (MID)

AF:

0.0156

AC:

AN:

128

European-Non Finnish (NFE)

AF:

0.103

AC:

1775

AN:

17314

Other (OTH)

AF:

0.0749

AC:

124

AN:

1656

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

107

214

321

428

535

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

110

<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:

0.0786

AC:

11972

AN:

152254

Hom.:

595

Cov.:

AF XY:

0.0788

AC XY:

5868

AN XY:

74454

show subpopulations

African (AFR)

AF:

0.0469

AC:

1951

AN:

41560

American (AMR)

AF:

0.0440

AC:

673

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.110

AC:

381

AN:

3470

East Asian (EAS)

AF:

0.00193

AC:

AN:

5182

South Asian (SAS)

AF:

0.0568

AC:

274

AN:

4824

European-Finnish (FIN)

AF:

0.107

AC:

1137

AN:

10614

Middle Eastern (MID)

AF:

0.0170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.108

AC:

7349

AN:

67990

Other (OTH)

AF:

0.0464

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

561

1121

1682

2242

2803

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

138

276

414

552

690

<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:

0.0863

Hom.:

850

Bravo

AF:

0.0708

Asia WGS

AF:

0.0290

AC:

101

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.053

(source)

DANN

Benign

0.35

PhyloP100

-4.2

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over