rs884970

chr10-119364989-A-Gchr10-119364989-A-T

Variant summary

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

The NM_005308.3(GRK5):c.149-15826A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 151,954 control chromosomes in the GnomAD database, including 17,663 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 0.47 (17663 hom., cov: 31)
• Consequence: GRK5 NM_005308.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GRK5	NM_005308.3	c.149-15826A>G		intron_variant		ENST00000392870.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRK5	ENST00000392870.3	c.149-15826A>G		intron_variant		1	NM_005308.3	P1

Frequencies

GnomAD3 genomes AF: 0.468 AC: 70993 AN: 151836 Hom.: 17658 Cov.: 31

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.467 AC: 71021 AN: 151954 Hom.: 17663 Cov.: 31 AF XY: 0.468 AC XY: 34758 AN XY: 74258

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.613

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.497

Alfa AF: 0.508 Hom.: 6218

Bravo AF: 0.462

Asia WGS AF: 0.435 AC: 1517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.3
Dann	Benign	0.58

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: rs884970; hg19: chr10-121124501;