rs4900318

Variant names:

• chr14-96222623-A-C
• rs4900318
• NM_001379692.1:c.-39-14446A>C

Your query was ambiguous. Multiple possible variants found:

• chr14-96222623-A-C
• chr14-96222623-A-G
• chr14-96222623-A-T

Variant summary

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

The NM_001379692.1(BDKRB2):​c.-39-14446A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 151,778 control chromosomes in the GnomAD database, including 22,282 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 0.54 (22282 hom., cov: 32)
• Consequence: BDKRB2 NM_001379692.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337
• Publications: 6 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.585 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BDKRB2	NM_001379692.1	MANE Select	c.-39-14446A>C		intron	N/A	NP_001366621.1
	BDKRB2	NM_000623.4		c.-34-14451A>C		intron	N/A	NP_000614.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BDKRB2	ENST00000554311.2	TSL:1 MANE Select	c.-39-14446A>C		intron	N/A	ENSP00000450482.1
	BDKRB2	ENST00000542454.2	TSL:1	c.-2807-14446A>C		intron	N/A	ENSP00000439459.2
	ENSG00000258691	ENST00000553811.1	TSL:2	c.-34-14451A>C		intron	N/A	ENSP00000450984.1

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81591 AN: 151660 Hom.: 22280 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.538 AC: 81615 AN: 151778 Hom.: 22282 Cov.: 32 AF XY: 0.535 AC XY: 39690 AN XY: 74164

African (AFR) AF: 0.453 AC: 18713 AN: 41306

American (AMR) AF: 0.516 AC: 7877 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1907 AN: 3466

East Asian (EAS) AF: 0.520 AC: 2688 AN: 5168

South Asian (SAS) AF: 0.521 AC: 2504 AN: 4802

European-Finnish (FIN) AF: 0.565 AC: 5947 AN: 10528

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.590 AC: 40051 AN: 67930

Other (OTH) AF: 0.551 AC: 1162 AN: 2108

Alfa AF: 0.546 Hom.: 3433

Bravo AF: 0.533

Asia WGS AF: 0.526 AC: 1834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.9
DANN	Benign	0.60
PhyloP100		-0.34
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: rs4900318; hg19: chr14-96688960;