rs4900312

Positions:

• chr14-96212637-A-G

Variant summary

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

The NM_001379692.1(BDKRB2):​c.-40+7678A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.767 in 152,140 control chromosomes in the GnomAD database, including 45,230 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 0.77 (45230 hom., cov: 31)
• Consequence: BDKRB2 NM_001379692.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.20

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.1).
• 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/exons	MANE	UniProt
BDKRB2	NM_001379692.1	c.-40+7678A>G		intron_variant		ENST00000554311.2
BDKRB2	NM_000623.4	c.-35+7678A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BDKRB2	ENST00000554311.2	c.-40+7678A>G		intron_variant		1	NM_001379692.1	P1
BDKRB2	ENST00000542454.2	c.-2808+7678A>G		intron_variant		1
	ENST00000555383.1	n.280+1498A>G		intron_variant, non_coding_transcript_variant		5
BDKRB2	ENST00000539359.1	c.-282+7678A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116698 AN: 152022 Hom.: 45214 Cov.: 31

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.863

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.767 AC: 116761 AN: 152140 Hom.: 45230 Cov.: 31 AF XY: 0.770 AC XY: 57231 AN XY: 74370

Gnomad4 AFR AF: 0.690

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.757

Gnomad4 EAS AF: 0.976

Gnomad4 SAS AF: 0.830

Gnomad4 FIN AF: 0.863

Gnomad4 NFE AF: 0.798

Gnomad4 OTH AF: 0.775

Alfa AF: 0.788 Hom.: 62291

Bravo AF: 0.753

Asia WGS AF: 0.902 AC: 3136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.19
DANN	Benign	0.23

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: rs4900312; hg19: chr14-96678974;