ENST00000553356.1:c.769-1776T>C

Variant names:

• chr14-96266654-T-C
• rs875964
• ENST00000553356.1:c.769-1776T>C

Variant summary

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

The ENST00000553356.1(BDKRB1):​c.769-1776T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.862 in 152,092 control chromosomes in the GnomAD database, including 56,924 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 0.86 (56924 hom., cov: 30)
• Consequence: BDKRB1 ENST00000553356.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380
• Publications: 3 publications found

Genes affected

BDKRB1 (HGNC:1029): (bradykinin receptor B1) Bradykinin, a 9 aa peptide, is generated in pathophysiologic conditions such as inflammation, trauma, burns, shock, and allergy. The protein encoded by this gene belongs to the G-protein coupled receptor 1 family. Two types of G-protein coupled receptors have been found which bind bradykinin and mediate responses to these pathophysiologic conditions. The protein encoded by this gene is one of these receptors and is synthesized de novo following tissue injury. Receptor binding leads to an increase in the cytosolic calcium ion concentration, ultimately resulting in chronic and acute inflammatory responses. [provided by RefSeq, Aug 2020]

ENSG00000258793 (HGNC:58458):

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 (AFR) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BDKRB1-AS1	XR_007064322.1	n.212+1715A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BDKRB1	ENST00000553356.1	c.769-1776T>C		intron_variant	Intron 4 of 4	1		ENSP00000452064.1
ENSG00000258793	ENST00000553638.2	n.289+1715A>G		intron_variant	Intron 1 of 1	2
BDKRB1	ENST00000557122.1	n.530+1299T>C		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.862 AC: 131019 AN: 151974 Hom.: 56868 Cov.: 30

Gnomad AFR AF: 0.969

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.863

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

GnomAD4 genome AF: 0.862 AC: 131132 AN: 152092 Hom.: 56924 Cov.: 30 AF XY: 0.855 AC XY: 63572 AN XY: 74350

African (AFR) AF: 0.969 AC: 40207 AN: 41494

American (AMR) AF: 0.812 AC: 12412 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.835 AC: 2900 AN: 3472

East Asian (EAS) AF: 0.737 AC: 3799 AN: 5152

South Asian (SAS) AF: 0.767 AC: 3685 AN: 4806

European-Finnish (FIN) AF: 0.778 AC: 8237 AN: 10588

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.839 AC: 57014 AN: 67976

Other (OTH) AF: 0.865 AC: 1826 AN: 2112

Alfa AF: 0.843 Hom.: 30483

Bravo AF: 0.873

Asia WGS AF: 0.776 AC: 2700 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	1.7
DANN	Benign	0.57
PhyloP100		-0.038
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs875964; hg19: chr14-96732991;