rs4905474
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001379692.1(BDKRB2):c.-39-6042G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,064 control chromosomes in the GnomAD database, including 4,627 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 0.24 ( 4627 hom., cov: 33)
Consequence
BDKRB2
NM_001379692.1 intron
NM_001379692.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.82
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BDKRB2 | NM_001379692.1 | c.-39-6042G>A | intron_variant | ENST00000554311.2 | |||
BDKRB2 | NM_000623.4 | c.-34-6047G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BDKRB2 | ENST00000554311.2 | c.-39-6042G>A | intron_variant | 1 | NM_001379692.1 | P1 | |||
BDKRB2 | ENST00000542454.2 | c.-2807-6042G>A | intron_variant | 1 | |||||
BDKRB2 | ENST00000539359.1 | c.-281-6047G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.242 AC: 36714AN: 151946Hom.: 4617 Cov.: 33
GnomAD3 genomes
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151946
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.242 AC: 36760AN: 152064Hom.: 4627 Cov.: 33 AF XY: 0.245 AC XY: 18201AN XY: 74328
GnomAD4 genome
?
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36760
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152064
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33
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18201
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74328
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1152
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at