Genetic Variant BDKRB1:c.-129-236A>G (chr14-96262416-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 NM_000710.4(BDKRB1):c.-129-236A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 152,038 control chromosomes in the GnomAD database, including 3,826 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 0.22 ( 3826 hom., cov: 31)

Consequence

BDKRB1
NM_000710.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.111

Publications

15 publications found

Variant links:

Genes affected

BDKRB1 (HGNC:1029): (bradykinin receptor B1) Bradykinin, a 9 aa peptide, is generated in pathophysiologic conditions such as inflammation, trauma, burns, shock, and allergy. The protein encoded by this gene belongs to the G-protein coupled receptor 1 family. Two types of G-protein coupled receptors have been found which bind bradykinin and mediate responses to these pathophysiologic conditions. The protein encoded by this gene is one of these receptors and is synthesized de novo following tissue injury. Receptor binding leads to an increase in the cytosolic calcium ion concentration, ultimately resulting in chronic and acute inflammatory responses. [provided by RefSeq, Aug 2020]

BDKRB1 links:

ENSG00000258691 (HGNC:):

ENSG00000258691 links:

BDKRB1-AS1 (HGNC:58458):

BDKRB1-AS1 links:

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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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
BDKRB1	NM_000710.4 link	c.-129-236A>G	intron_variant	Intron 1 of 2	ENST00000216629.11	NP_000701.2
BDKRB1-AS1	XR_007064323.1 link	n.196T>C	non_coding_transcript_exon_variant	Exon 1 of 2
BDKRB1	NM_001386007.1 link	c.-10-1257A>G	intron_variant	Intron 1 of 1		NP_001372936.1
BDKRB1-AS1	XR_007064322.1 link	n.213-2524T>C	intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BDKRB1	ENST00000216629.11 link	c.-129-236A>G		intron_variant	Intron 1 of 2	1	NM_000710.4	ENSP00000216629.6
ENSG00000258691	ENST00000553811.1 link	c.75-236A>G		intron_variant	Intron 2 of 3	2		ENSP00000450984.1

Frequencies

GnomAD3 genomes

AF:

0.218

AC:

33076

AN:

151920

Hom.:

3824

Cov.:

show subpopulations

Gnomad AFR

AF:

0.184

Gnomad AMI

AF:

0.242

Gnomad AMR

AF:

0.310

Gnomad ASJ

AF:

0.208

Gnomad EAS

AF:

0.414

Gnomad SAS

AF:

0.171

Gnomad FIN

AF:

0.214

Gnomad MID

AF:

0.199

Gnomad NFE

AF:

0.206

Gnomad OTH

AF:

0.242

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.218

AC:

33083

AN:

152038

Hom.:

3826

Cov.:

AF XY:

0.218

AC XY:

16196

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.183

AC:

7602

AN:

41470

American (AMR)

AF:

0.310

AC:

4737

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.208

AC:

723

AN:

3468

East Asian (EAS)

AF:

0.413

AC:

2132

AN:

5160

South Asian (SAS)

AF:

0.170

AC:

820

AN:

4812

European-Finnish (FIN)

AF:

0.214

AC:

2266

AN:

10572

Middle Eastern (MID)

AF:

0.194

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.206

AC:

14017

AN:

67970

Other (OTH)

AF:

0.241

AC:

509

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1280

2560

3839

5119

6399

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

344

688

1032

1376

1720

<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:

0.212

Hom.:

16391

Bravo

AF:

0.227

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.3

(source)

DANN

Benign

0.42

PhyloP100

-0.11

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over