10-119314727-T-A

Position:

• chr10-119314727-T-A

Variant summary

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

The NM_005308.3(GRK5):​c.53-11789T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 152,094 control chromosomes in the GnomAD database, including 38,171 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 0.69 (38171 hom., cov: 32)
• Consequence: GRK5 NM_005308.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GRK5	NM_005308.3	c.53-11789T>A		intron_variant		ENST00000392870.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRK5	ENST00000392870.3	c.53-11789T>A		intron_variant		1	NM_005308.3	P1

Frequencies

GnomAD3 genomes AF: 0.694 AC: 105428 AN: 151976 Hom.: 38147 Cov.: 32

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.694 AC: 105497 AN: 152094 Hom.: 38171 Cov.: 32 AF XY: 0.696 AC XY: 51769 AN XY: 74340

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.719

Gnomad4 ASJ AF: 0.793

Gnomad4 EAS AF: 0.703

Gnomad4 SAS AF: 0.731

Gnomad4 FIN AF: 0.839

Gnomad4 NFE AF: 0.789

Gnomad4 OTH AF: 0.696

Alfa AF: 0.738 Hom.: 5293

Bravo AF: 0.674

Asia WGS AF: 0.729 AC: 2536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.28
DANN	Benign	0.55

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: rs915394; hg19: chr10-121074239;