rs4752266

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005308.3(GRK5):​c.52+47646G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.67 in 152,044 control chromosomes in the GnomAD database, including 35,452 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 0.67 ( 35452 hom., cov: 31)

Consequence

GRK5
NM_005308.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.159
Variant links:
Genes affected
GRK5 (HGNC:4544): (G protein-coupled receptor kinase 5) This gene encodes a member of the guanine nucleotide-binding protein (G protein)-coupled receptor kinase subfamily of the Ser/Thr protein kinase family. The protein phosphorylates the activated forms of G protein-coupled receptors thus initiating their deactivation. It has also been shown to play a role in regulating the motility of polymorphonuclear leukocytes (PMNs). [provided by RefSeq, Jul 2008]

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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=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GRK5NM_005308.3 linkuse as main transcriptc.52+47646G>A intron_variant ENST00000392870.3
GRK5XM_005269707.3 linkuse as main transcriptc.52+47646G>A intron_variant
GRK5XM_005269708.2 linkuse as main transcriptc.52+47646G>A intron_variant
GRK5XM_047425120.1 linkuse as main transcriptc.-264+46965G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GRK5ENST00000392870.3 linkuse as main transcriptc.52+47646G>A intron_variant 1 NM_005308.3 P1

Frequencies

GnomAD3 genomes
AF:
0.670
AC:
101828
AN:
151926
Hom.:
35448
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.472
Gnomad AMI
AF:
0.898
Gnomad AMR
AF:
0.651
Gnomad ASJ
AF:
0.759
Gnomad EAS
AF:
0.832
Gnomad SAS
AF:
0.791
Gnomad FIN
AF:
0.791
Gnomad MID
AF:
0.728
Gnomad NFE
AF:
0.748
Gnomad OTH
AF:
0.683
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.670
AC:
101871
AN:
152044
Hom.:
35452
Cov.:
31
AF XY:
0.673
AC XY:
50004
AN XY:
74296
show subpopulations
Gnomad4 AFR
AF:
0.471
Gnomad4 AMR
AF:
0.651
Gnomad4 ASJ
AF:
0.759
Gnomad4 EAS
AF:
0.833
Gnomad4 SAS
AF:
0.791
Gnomad4 FIN
AF:
0.791
Gnomad4 NFE
AF:
0.748
Gnomad4 OTH
AF:
0.685
Alfa
AF:
0.710
Hom.:
4919
Bravo
AF:
0.645
Asia WGS
AF:
0.757
AC:
2632
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.84
DANN
Benign
0.55
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4752266; hg19: chr10-121015127; API