14-96204324-T-C

Variant names:

• chr14-96204324-T-C
• rs945032
• ENST00000877850.1:c.-670T>C

Variant summary

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

The ENST00000877850.1(BDKRB2):​c.-670T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.789 in 151,950 control chromosomes in the GnomAD database, including 47,671 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 0.79 (47671 hom., cov: 30)
• Consequence: BDKRB2 ENST00000877850.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102
• Publications: 20 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000877850.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BDKRB2	ENST00000877850.1		c.-670T>C		upstream_gene	N/A	ENSP00000547909.1

Frequencies

GnomAD3 genomes AF: 0.789 AC: 119772 AN: 151830 Hom.: 47650 Cov.: 30

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.895

Gnomad AMR AF: 0.870

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.815

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.789 AC: 119841 AN: 151950 Hom.: 47671 Cov.: 30 AF XY: 0.791 AC XY: 58719 AN XY: 74276

African (AFR) AF: 0.681 AC: 28163 AN: 41378

American (AMR) AF: 0.870 AC: 13288 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.766 AC: 2658 AN: 3468

East Asian (EAS) AF: 0.868 AC: 4468 AN: 5146

South Asian (SAS) AF: 0.839 AC: 4035 AN: 4810

European-Finnish (FIN) AF: 0.852 AC: 9014 AN: 10578

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.816 AC: 55503 AN: 67982

Other (OTH) AF: 0.785 AC: 1657 AN: 2112

Alfa AF: 0.805 Hom.: 161133

Bravo AF: 0.781

Asia WGS AF: 0.821 AC: 2853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.92
DANN	Benign	0.30
PhyloP100		-0.10
PromoterAI		0.0033	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs945032; hg19: chr14-96670661;