rs4900318

Positions:

• chr14-96222623-A-C
• chr14-96222623-A-G
• chr14-96222623-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001379692.1(BDKRB2):​c.-39-14446A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 151,778 control chromosomes in the GnomAD database, including 22,282 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 0.54 (22282 hom., cov: 32)
• Consequence: BDKRB2 NM_001379692.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BDKRB2	NM_001379692.1	c.-39-14446A>C		intron_variant		ENST00000554311.2	NP_001366621.1
BDKRB2	NM_000623.4	c.-34-14451A>C		intron_variant			NP_000614.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BDKRB2	ENST00000554311.2	c.-39-14446A>C		intron_variant		1	NM_001379692.1	ENSP00000450482	P1
BDKRB2	ENST00000542454.2	c.-2807-14446A>C		intron_variant		1		ENSP00000439459
BDKRB2	ENST00000539359.1	c.-281-14451A>C		intron_variant		2		ENSP00000438376

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81591 AN: 151660 Hom.: 22280 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.538 AC: 81615 AN: 151778 Hom.: 22282 Cov.: 32 AF XY: 0.535 AC XY: 39690 AN XY: 74164

Gnomad4 AFR AF: 0.453

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.521

Gnomad4 FIN AF: 0.565

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.551

Alfa AF: 0.549 Hom.: 3350

Bravo AF: 0.533

Asia WGS AF: 0.526 AC: 1834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.9
DANN	Benign	0.60

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

LitVar

Other links and lift over

dbSNP: rs4900318; hg19: chr14-96688960;