Variant rs11198918 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_005308.3(GRK5):c.340-98T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0708 in 773,052 control chromosomes in the GnomAD database, including 2,899 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 0.055 ( 405 hom., cov: 33)

Exomes 𝑓: 0.075 ( 2494 hom. )

Consequence

GRK5
NM_005308.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.17

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]

GRK5 links:

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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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GRK5	NM_005308.3 linkuse as main transcript	c.340-98T>C		intron_variant		ENST00000392870.3	NP_005299.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GRK5	ENST00000392870.3 linkuse as main transcript	c.340-98T>C		intron_variant		1	NM_005308.3	ENSP00000376609	P1

Frequencies

GnomAD3 genomes

AF:

0.0547

AC:

8321

AN:

152178

Hom.:

406

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0127

Gnomad AMI

AF:

0.0406

Gnomad AMR

AF:

0.0427

Gnomad ASJ

AF:

0.0369

Gnomad EAS

AF:

0.232

Gnomad SAS

AF:

0.155

Gnomad FIN

AF:

0.0477

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0650

Gnomad OTH

AF:

0.0463

GnomAD4 exome

AF:

0.0748

AC:

46407

AN:

620756

Hom.:

2494

AF XY:

0.0784

AC XY:

26064

AN XY:

332262

show subpopulations

Gnomad4 AFR exome

AF:

0.0127

Gnomad4 AMR exome

AF:

0.0425

Gnomad4 ASJ exome

AF:

0.0374

Gnomad4 EAS exome

AF:

0.209

Gnomad4 SAS exome

AF:

0.145

Gnomad4 FIN exome

AF:

0.0474

Gnomad4 NFE exome

AF:

0.0623

Gnomad4 OTH exome

AF:

0.0675

GnomAD4 genome

AF:

0.0546

AC:

8320

AN:

152296

Hom.:

405

Cov.:

AF XY:

0.0563

AC XY:

4195

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.0126

Gnomad4 AMR

AF:

0.0426

Gnomad4 ASJ

AF:

0.0369

Gnomad4 EAS

AF:

0.232

Gnomad4 SAS

AF:

0.155

Gnomad4 FIN

AF:

0.0477

Gnomad4 NFE

AF:

0.0650

Gnomad4 OTH

AF:

0.0468

Alfa

AF:

0.0586

Hom.:

Bravo

AF:

0.0501

Asia WGS

AF:

0.142

AC:

494

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.31

DANN

Benign

0.56

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over