14-96222271-T-C

Variant names:

• chr14-96222271-T-C
• rs8013400
• NM_001379692.1:c.-39-14798T>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.-39-14798T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.74 in 151,992 control chromosomes in the GnomAD database, including 42,301 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 0.74 (42301 hom., cov: 33)
• Consequence: BDKRB2 NM_001379692.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250
• Publications: 7 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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001379692.1. 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
	BDKRB2	NM_001379692.1	MANE Select	c.-39-14798T>C		intron	N/A	NP_001366621.1	P30411-1
	BDKRB2	NM_000623.4		c.-34-14803T>C		intron	N/A	NP_000614.1	P30411-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BDKRB2	ENST00000554311.2	TSL:1 MANE Select	c.-39-14798T>C		intron	N/A	ENSP00000450482.1	P30411-1
	BDKRB2	ENST00000542454.2	TSL:1	c.-2807-14798T>C		intron	N/A	ENSP00000439459.2	P30411-2
	ENSG00000258691	ENST00000553811.1	TSL:2	c.-34-14803T>C		intron	N/A	ENSP00000450984.1	G3V318

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112396 AN: 151876 Hom.: 42307 Cov.: 33

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.740 AC: 112417 AN: 151992 Hom.: 42301 Cov.: 33 AF XY: 0.739 AC XY: 54866 AN XY: 74286

African (AFR) AF: 0.615 AC: 25410 AN: 41340

American (AMR) AF: 0.667 AC: 10190 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 2601 AN: 3472

East Asian (EAS) AF: 0.723 AC: 3729 AN: 5160

South Asian (SAS) AF: 0.786 AC: 3781 AN: 4810

European-Finnish (FIN) AF: 0.797 AC: 8451 AN: 10606

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.819 AC: 55699 AN: 68006

Other (OTH) AF: 0.739 AC: 1563 AN: 2114

Alfa AF: 0.789 Hom.: 142032

Bravo AF: 0.724

Asia WGS AF: 0.749 AC: 2607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.7
DANN	Benign	0.60
PhyloP100		-0.25
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: rs8013400; hg19: chr14-96688608;