Variant rs7099478 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.738+147C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 942,410 control chromosomes in the GnomAD database, including 135,137 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 0.57 ( 25872 hom., cov: 33)

Exomes 𝑓: 0.52 ( 109265 hom. )

Consequence

GRK5
NM_005308.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.30

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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.683 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.738+147C>A		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.738+147C>A		intron_variant		1	NM_005308.3	ENSP00000376609	P1

Frequencies

GnomAD3 genomes

AF:

0.575

AC:

87365

AN:

152044

Hom.:

25831

Cov.:

show subpopulations

Gnomad AFR

AF:

0.689

Gnomad AMI

AF:

0.616

Gnomad AMR

AF:

0.631

Gnomad ASJ

AF:

0.562

Gnomad EAS

AF:

0.320

Gnomad SAS

AF:

0.448

Gnomad FIN

AF:

0.595

Gnomad MID

AF:

0.570

Gnomad NFE

AF:

0.518

Gnomad OTH

AF:

0.543

GnomAD4 exome

AF:

0.517

AC:

408853

AN:

790248

Hom.:

109265

AF XY:

0.516

AC XY:

205200

AN XY:

397818

show subpopulations

Gnomad4 AFR exome

AF:

0.677

Gnomad4 AMR exome

AF:

0.673

Gnomad4 ASJ exome

AF:

0.545

Gnomad4 EAS exome

AF:

0.324

Gnomad4 SAS exome

AF:

0.451

Gnomad4 FIN exome

AF:

0.591

Gnomad4 NFE exome

AF:

0.517

Gnomad4 OTH exome

AF:

0.535

GnomAD4 genome

AF:

0.575

AC:

87461

AN:

152162

Hom.:

25872

Cov.:

AF XY:

0.575

AC XY:

42761

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.690

Gnomad4 AMR

AF:

0.631

Gnomad4 ASJ

AF:

0.562

Gnomad4 EAS

AF:

0.320

Gnomad4 SAS

AF:

0.448

Gnomad4 FIN

AF:

0.595

Gnomad4 NFE

AF:

0.518

Gnomad4 OTH

AF:

0.543

Alfa

AF:

0.515

Hom.:

33472

Bravo

AF:

0.586

Asia WGS

AF:

0.455

AC:

1585

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.36

DANN

Benign

0.73

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