rs945039

Variant names:

• chr14-96217861-A-G
• rs945039
• NM_001379692.1:c.-40+12902A>G

Your query was ambiguous. Multiple possible variants found:

• chr14-96217861-A-G
• chr14-96217861-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.-40+12902A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 151,420 control chromosomes in the GnomAD database, including 35,918 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 0.68 (35918 hom., cov: 31)
• Consequence: BDKRB2 NM_001379692.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BDKRB2	NM_001379692.1	c.-40+12902A>G		intron_variant	Intron 1 of 2	ENST00000554311.2	NP_001366621.1
BDKRB2	NM_000623.4	c.-35+12902A>G		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+12902A>G		intron_variant	Intron 1 of 2	1	NM_001379692.1	ENSP00000450482.1
BDKRB2	ENST00000542454.2	c.-2808+12902A>G		intron_variant	Intron 1 of 2	1		ENSP00000439459.2
ENSG00000258691	ENST00000553811.1	c.-35+12902A>G		intron_variant	Intron 1 of 3	2		ENSP00000450984.1
BDKRB2	ENST00000539359.1	c.-282+12902A>G		intron_variant	Intron 1 of 3	2		ENSP00000438376.1

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103444 AN: 151304 Hom.: 35919 Cov.: 31

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.778

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.683 AC: 103466 AN: 151420 Hom.: 35918 Cov.: 31 AF XY: 0.683 AC XY: 50515 AN XY: 74012

Gnomad4 AFR AF: 0.575

Gnomad4 AMR AF: 0.638

Gnomad4 ASJ AF: 0.671

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.736

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.752

Gnomad4 OTH AF: 0.687

Alfa AF: 0.732 Hom.: 32275

Bravo AF: 0.670

Asia WGS AF: 0.658 AC: 2290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.98
DANN	Benign	0.55

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: rs945039; hg19: chr14-96684198;