14-96242445-A-T

Variant names:

• chr14-96242445-A-T
• rs2069590
• NM_001379692.1:c.*941A>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001379692.1(BDKRB2):​c.*941A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 152,226 control chromosomes in the GnomAD database, including 5,733 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 0.27 (5733 hom., cov: 34)
  • Exomes 𝑓: 0.30 (0 hom.)
• Consequence: BDKRB2 NM_001379692.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BDKRB2	NM_001379692.1	c.*941A>T		3_prime_UTR_variant	Exon 3 of 3	ENST00000554311.2	NP_001366621.1
BDKRB2	NM_000623.4	c.*941A>T		3_prime_UTR_variant	Exon 3 of 3		NP_000614.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BDKRB2	ENST00000554311.2	c.*941A>T		3_prime_UTR_variant	Exon 3 of 3	1	NM_001379692.1	ENSP00000450482.1
BDKRB2	ENST00000542454.2	c.*941A>T		3_prime_UTR_variant	Exon 3 of 3	1		ENSP00000439459.2
ENSG00000258691	ENST00000553811.1	c.74+5264A>T		intron_variant	Intron 2 of 3	2		ENSP00000450984.1
ENSG00000258691	ENST00000555847.1	n.255+50A>T		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41090 AN: 152098 Hom.: 5736 Cov.: 34

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.306

GnomAD4 exome AF: 0.300 AC: 3 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 2 AN XY: 8

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.270 AC: 41097 AN: 152216 Hom.: 5733 Cov.: 34 AF XY: 0.269 AC XY: 20006 AN XY: 74426

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.304

Alfa AF: 0.263 Hom.: 3117

Bravo AF: 0.282

Asia WGS AF: 0.292 AC: 1020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.012
DANN	Benign	0.53

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

Publications

LitVar

Other links and lift over

dbSNP: rs2069590; hg19: chr14-96708782;