Genetic Variant BDKRB2:c.-110_-102delGGTGGGGAC (chr14-96204870-GGGTGGGGAC-G) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001379692.1(BDKRB2):c.-110_-102delGGTGGGGAC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 344,246 control chromosomes in the GnomAD database, including 46,554 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.50 ( 20120 hom., cov: 0)

Exomes 𝑓: 0.50 ( 26434 hom. )

Consequence

BDKRB2
NM_001379692.1 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00

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 -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) 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
BDKRB2	NM_001379692.1 link	c.-110_-102delGGTGGGGAC		5_prime_UTR_variant	Exon 1 of 3	ENST00000554311.2	NP_001366621.1
BDKRB2	NM_000623.4 link	c.-105_-97delGGTGGGGAC		5_prime_UTR_variant	Exon 1 of 3		NP_000614.1	P30411-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
BDKRB2	ENST00000554311 link	c.-110_-102delGGTGGGGAC	5_prime_UTR_variant	Exon 1 of 3	1	NM_001379692.1	ENSP00000450482.1	P30411-1
BDKRB2	ENST00000542454 link	c.-2878_-2870delGGTGGGGAC	5_prime_UTR_variant	Exon 1 of 3	1		ENSP00000439459.2	P30411-2
ENSG00000258691	ENST00000553811 link	c.-105_-97delGGTGGGGAC	5_prime_UTR_variant	Exon 1 of 4	2		ENSP00000450984.1	G3V318
BDKRB2	ENST00000539359 link	c.-352_-344delGGTGGGGAC	5_prime_UTR_variant	Exon 1 of 4	2		ENSP00000438376.1	P30411-2

Frequencies

GnomAD3 genomes

AF:

0.502

AC:

75994

AN:

151234

Hom.:

20082

Cov.:

show subpopulations

Gnomad AFR

AF:

0.436

Gnomad AMI

AF:

0.341

Gnomad AMR

AF:

0.617

Gnomad ASJ

AF:

0.472

Gnomad EAS

AF:

0.977

Gnomad SAS

AF:

0.673

Gnomad FIN

AF:

0.497

Gnomad MID

AF:

0.439

Gnomad NFE

AF:

0.475

Gnomad OTH

AF:

0.509

GnomAD2 exomes

AF:

0.435

AC:

17474

AN:

40160

AF XY:

0.429

show subpopulations

Gnomad AFR exome

AF:

0.317

Gnomad AMR exome

AF:

0.593

Gnomad ASJ exome

AF:

0.289

Gnomad EAS exome

AF:

0.956

Gnomad FIN exome

AF:

0.359

Gnomad NFE exome

AF:

0.354

Gnomad OTH exome

AF:

0.376

GnomAD4 exome

AF:

0.496

AC:

95614

AN:

192894

Hom.:

26434

AF XY:

0.505

AC XY:

56640

AN XY:

112054

show subpopulations

Gnomad4 AFR exome

AF:

0.343

AC:

1191

AN:

3468

Gnomad4 AMR exome

AF:

0.633

AC:

7278

AN:

11492

Gnomad4 ASJ exome

AF:

0.387

AC:

2159

AN:

5582

Gnomad4 EAS exome

AF:

0.971

AC:

2526

AN:

2602

Gnomad4 SAS exome

AF:

0.617

AC:

26211

AN:

42514

Gnomad4 FIN exome

AF:

0.490

AC:

4846

AN:

9888

Gnomad4 NFE exome

AF:

0.435

AC:

46287

AN:

106324

Gnomad4 Remaining exome

AF:

0.469

AC:

4209

AN:

8982

Heterozygous variant carriers

1723

3446

5169

6892

8615

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

234

468

702

936

1170

<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:

0.503

AC:

76079

AN:

151352

Hom.:

20120

Cov.:

AF XY:

0.512

AC XY:

37838

AN XY:

73936

show subpopulations

Gnomad4 AFR

AF:

0.436

AC:

0.436163

AN:

0.436163

Gnomad4 AMR

AF:

0.617

AC:

0.617361

AN:

0.617361

Gnomad4 ASJ

AF:

0.472

AC:

0.472206

AN:

0.472206

Gnomad4 EAS

AF:

0.977

AC:

0.976795

AN:

0.976795

Gnomad4 SAS

AF:

0.674

AC:

0.673631

AN:

0.673631

Gnomad4 FIN

AF:

0.497

AC:

0.497235

AN:

0.497235

Gnomad4 NFE

AF:

0.475

AC:

0.47456

AN:

0.47456

Gnomad4 OTH

AF:

0.515

AC:

0.514678

AN:

0.514678

Heterozygous variant carriers

1738

3476

5213

6951

8689

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

678

1356

2034

2712

3390

<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:

0.356

Hom.:

1629

Bravo

AF:

0.511

Asia WGS

AF:

0.814

AC:

2826

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Mutation Taster

=300/0

polymorphism (auto)

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over