rs2420616

Variant names:

• chr10-119316984-A-G
• rs2420616
• NM_005308.3:c.53-9532A>G

Your query was ambiguous. Multiple possible variants found:

• chr10-119316984-A-G
• chr10-119316984-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005308.3(GRK5):​c.53-9532A>G 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 152,084 control chromosomes in the GnomAD database, including 38,256 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 (38256 hom., cov: 32)
• Consequence: GRK5 NM_005308.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GRK5	NM_005308.3	c.53-9532A>G		intron_variant	Intron 1 of 15	ENST00000392870.3	NP_005299.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRK5	ENST00000392870.3	c.53-9532A>G		intron_variant	Intron 1 of 15	1	NM_005308.3	ENSP00000376609.2

Frequencies

GnomAD3 genomes AF: 0.695 AC: 105545 AN: 151966 Hom.: 38232 Cov.: 32

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.694 AC: 105614 AN: 152084 Hom.: 38256 Cov.: 32 AF XY: 0.697 AC XY: 51849 AN XY: 74342

African (AFR) AF: 0.474 AC: 19648 AN: 41462

American (AMR) AF: 0.721 AC: 11017 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2776 AN: 3472

East Asian (EAS) AF: 0.704 AC: 3635 AN: 5166

South Asian (SAS) AF: 0.730 AC: 3507 AN: 4802

European-Finnish (FIN) AF: 0.839 AC: 8900 AN: 10602

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.790 AC: 53683 AN: 67982

Other (OTH) AF: 0.699 AC: 1477 AN: 2114

Alfa AF: 0.693 Hom.: 2591

Bravo AF: 0.675

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	-0.82
CADD	Benign	1.3
DANN	Benign	0.71
PhyloP100		-0.38
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2420616; hg19: chr10-121076496;