chr14-96204870-GGGTGGGGAC-G

Position:

• chr14-96204870-GGGTGGGGAC-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001379692.1(BDKRB2):​c.-110_-102del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 344,246 control chromosomes in the GnomAD database, including 46,554 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.50 (20120 hom., cov: 0)
  • Exomes 𝑓: 0.50 (26434 hom.)
• Consequence: BDKRB2 NM_001379692.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

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]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BDKRB2	NM_001379692.1	c.-110_-102del		5_prime_UTR_variant	1/3	ENST00000554311.2	NP_001366621.1
BDKRB2	NM_000623.4	c.-105_-97del		5_prime_UTR_variant	1/3		NP_000614.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BDKRB2	ENST00000554311.2	c.-110_-102del		5_prime_UTR_variant	1/3	1	NM_001379692.1	ENSP00000450482	P1
BDKRB2	ENST00000542454.2	c.-2878_-2870del		5_prime_UTR_variant	1/3	1		ENSP00000439459
BDKRB2	ENST00000539359.1	c.-352_-344del		5_prime_UTR_variant	1/4	2		ENSP00000438376

Frequencies

GnomAD3 genomes AF: 0.502 AC: 75994 AN: 151234 Hom.: 20082 Cov.: 0

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.509

GnomAD3 exomes AF: 0.435 AC: 17474 AN: 40160 Hom.: 4766 AF XY: 0.429 AC XY: 9394 AN XY: 21888

Gnomad AFR exome AF: 0.317

Gnomad AMR exome AF: 0.593

Gnomad ASJ exome AF: 0.289

Gnomad EAS exome AF: 0.956

Gnomad SAS exome AF: 0.507

Gnomad FIN exome AF: 0.359

Gnomad NFE exome AF: 0.354

Gnomad OTH exome AF: 0.376

GnomAD4 exome AF: 0.496 AC: 95614 AN: 192894 Hom.: 26434 AF XY: 0.505 AC XY: 56640 AN XY: 112054

Gnomad4 AFR exome AF: 0.343

Gnomad4 AMR exome AF: 0.633

Gnomad4 ASJ exome AF: 0.387

Gnomad4 EAS exome AF: 0.971

Gnomad4 SAS exome AF: 0.617

Gnomad4 FIN exome AF: 0.490

Gnomad4 NFE exome AF: 0.435

Gnomad4 OTH exome AF: 0.469

GnomAD4 genome AF: 0.503 AC: 76079 AN: 151352 Hom.: 20120 Cov.: 0 AF XY: 0.512 AC XY: 37838 AN XY: 73936

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.977

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.515

Alfa AF: 0.356 Hom.: 1629

Bravo AF: 0.511

Asia WGS AF: 0.814 AC: 2826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs71103505; hg19: chr14-96671207;