14-96264024-C-T

Variant names:

• chr14-96264024-C-T
• rs142760903
• NM_000710.4:c.342C>T

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_Strong BP7 BS2

The NM_000710.4(BDKRB1):​c.342C>T​(p.Asn114Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00234 in 1,614,096 control chromosomes in the GnomAD database, including 11 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 0.0016 (1 hom., cov: 33)
  • Exomes 𝑓: 0.0024 (10 hom.)
• Consequence: BDKRB1 NM_000710.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10
• Publications: 0 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):

ENSG00000258691 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BP7: Synonymous conserved (PhyloP=-2.1 with no splicing effect.
• BS2: High Homozygotes in GnomAdExome4 at 10 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000710.4. 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
	BDKRB1	NM_000710.4	MANE Select	c.342C>T	p.Asn114Asn	synonymous	Exon 3 of 3	NP_000701.2
	BDKRB1	NM_001386007.1		c.342C>T	p.Asn114Asn	synonymous	Exon 2 of 2	NP_001372936.1	P46663

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BDKRB1	ENST00000216629.11	TSL:1 MANE Select	c.342C>T	p.Asn114Asn	synonymous	Exon 3 of 3	ENSP00000216629.6	P46663
	BDKRB1	ENST00000553356.1	TSL:1	c.342C>T	p.Asn114Asn	synonymous	Exon 3 of 5	ENSP00000452064.1	G3V4Y2
	BDKRB1	ENST00000611804.1	TSL:6	c.342C>T	p.Asn114Asn	synonymous	Exon 1 of 1	ENSP00000479276.1	P46663

Frequencies

GnomAD3 genomes AF: 0.00160 AC: 243 AN: 152200 Hom.: 1 Cov.: 33

Gnomad AFR AF: 0.000362

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000523

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00104

Gnomad FIN AF: 0.00198

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00272

Gnomad OTH AF: 0.000478

GnomAD2 exomes AF: 0.00205 AC: 514 AN: 251286 AF XY: 0.00211

Gnomad AFR exome AF: 0.000431

Gnomad AMR exome AF: 0.000984

Gnomad ASJ exome AF: 0.00238

Gnomad EAS exome AF: 0.0000544

Gnomad FIN exome AF: 0.00263

Gnomad NFE exome AF: 0.00305

Gnomad OTH exome AF: 0.00212

GnomAD4 exome AF: 0.00242 AC: 3540 AN: 1461780 Hom.: 10 Cov.: 34 AF XY: 0.00240 AC XY: 1744 AN XY: 727190

African (AFR) AF: 0.000269 AC: 9 AN: 33480

American (AMR) AF: 0.000850 AC: 38 AN: 44714

Ashkenazi Jewish (ASJ) AF: 0.00188 AC: 49 AN: 26122

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.000951 AC: 82 AN: 86238

European-Finnish (FIN) AF: 0.00354 AC: 189 AN: 53416

Middle Eastern (MID) AF: 0.000173 AC: 1 AN: 5766

European-Non Finnish (NFE) AF: 0.00272 AC: 3021 AN: 1111954

Other (OTH) AF: 0.00250 AC: 151 AN: 60390

GnomAD4 genome AF: 0.00160 AC: 243 AN: 152316 Hom.: 1 Cov.: 33 AF XY: 0.00138 AC XY: 103 AN XY: 74476

African (AFR) AF: 0.000361 AC: 15 AN: 41570

American (AMR) AF: 0.000523 AC: 8 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.00202 AC: 7 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5176

South Asian (SAS) AF: 0.00104 AC: 5 AN: 4824

European-Finnish (FIN) AF: 0.00198 AC: 21 AN: 10620

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00272 AC: 185 AN: 68028

Other (OTH) AF: 0.000473 AC: 1 AN: 2112

Alfa AF: 0.00129 Hom.: 0

Bravo AF: 0.00145

Asia WGS AF: 0.000866 AC: 3 AN: 3478

EpiCase AF: 0.00191

EpiControl AF: 0.00213

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	0.27
DANN	Benign	0.87
PhyloP100		-2.1
PromoterAI		-0.031	Neutral
Mutation Taster		=100/0	polymorphism

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: rs142760903; hg19: chr14-96730361;