14-96219959-G-C

Variant names:

• chr14-96219959-G-C
• rs11847625
• NM_001379692.1:c.-40+15000G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001379692.1(BDKRB2):​c.-40+15000G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 151,834 control chromosomes in the GnomAD database, including 7,075 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 0.29 (7075 hom., cov: 31)
• Consequence: BDKRB2 NM_001379692.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 8 publications found

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]

ENSG00000258691 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BDKRB2	NM_001379692.1	c.-40+15000G>C		intron_variant	Intron 1 of 2	ENST00000554311.2	NP_001366621.1
BDKRB2	NM_000623.4	c.-35+15000G>C		intron_variant	Intron 1 of 2		NP_000614.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BDKRB2	ENST00000554311.2	c.-40+15000G>C		intron_variant	Intron 1 of 2	1	NM_001379692.1	ENSP00000450482.1
BDKRB2	ENST00000542454.2	c.-2808+15000G>C		intron_variant	Intron 1 of 2	1		ENSP00000439459.2
ENSG00000258691	ENST00000553811.1	c.-35+15000G>C		intron_variant	Intron 1 of 3	2		ENSP00000450984.1
BDKRB2	ENST00000539359.1	c.-282+15000G>C		intron_variant	Intron 1 of 3	2		ENSP00000438376.1

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43908 AN: 151714 Hom.: 7076 Cov.: 31

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.289 AC: 43903 AN: 151834 Hom.: 7075 Cov.: 31 AF XY: 0.284 AC XY: 21036 AN XY: 74182

African (AFR) AF: 0.155 AC: 6414 AN: 41342

American (AMR) AF: 0.287 AC: 4380 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1287 AN: 3470

East Asian (EAS) AF: 0.242 AC: 1244 AN: 5150

South Asian (SAS) AF: 0.256 AC: 1226 AN: 4798

European-Finnish (FIN) AF: 0.271 AC: 2862 AN: 10568

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25360 AN: 67940

Other (OTH) AF: 0.341 AC: 718 AN: 2108

Alfa AF: 0.206 Hom.: 514

Bravo AF: 0.289

Asia WGS AF: 0.236 AC: 828 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.44
PhyloP100		0.011
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11847625; hg19: chr14-96686296;