chr10-119342186-C-T

Position:

• chr10-119342186-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005308.3(GRK5):​c.148+15575C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.747 in 152,196 control chromosomes in the GnomAD database, including 44,797 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 0.75 (44797 hom., cov: 33)
• Consequence: GRK5 NM_005308.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GRK5	NM_005308.3	c.148+15575C>T		intron_variant		ENST00000392870.3	NP_005299.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GRK5	ENST00000392870.3	c.148+15575C>T		intron_variant		1	NM_005308.3	ENSP00000376609	P1

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113614 AN: 152078 Hom.: 44792 Cov.: 33

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.955

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.862

Gnomad OTH AF: 0.779

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.747 AC: 113649 AN: 152196 Hom.: 44797 Cov.: 33 AF XY: 0.749 AC XY: 55736 AN XY: 74426

Gnomad4 AFR AF: 0.471

Gnomad4 AMR AF: 0.835

Gnomad4 ASJ AF: 0.908

Gnomad4 EAS AF: 0.709

Gnomad4 SAS AF: 0.766

Gnomad4 FIN AF: 0.887

Gnomad4 NFE AF: 0.862

Gnomad4 OTH AF: 0.780

Alfa AF: 0.794 Hom.: 6139

Bravo AF: 0.730

Asia WGS AF: 0.755 AC: 2625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.5
DANN	Benign	0.42

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

Other links and lift over

dbSNP: rs4752293; hg19: chr10-121101698;