rs11198856

Variant names:

• chr10-119282186-C-A
• rs11198856
• NM_005308.3:c.53-44330C>A

Your query was ambiguous. Multiple possible variants found:

• chr10-119282186-C-A
• chr10-119282186-C-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.53-44330C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,136 control chromosomes in the GnomAD database, including 6,804 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 0.28 (6804 hom., cov: 32)
• Consequence: GRK5 NM_005308.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.856
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005308.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GRK5	NM_005308.3	MANE Select	c.53-44330C>A		intron	N/A	NP_005299.1	P34947

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GRK5	ENST00000392870.3	TSL:1 MANE Select	c.53-44330C>A		intron	N/A	ENSP00000376609.2	P34947
	GRK5	ENST00000857196.1		c.53-44330C>A		intron	N/A	ENSP00000527255.1
	GRK5	ENST00000857197.1		c.53-44330C>A		intron	N/A	ENSP00000527256.1

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41942 AN: 152020 Hom.: 6800 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.276 AC: 41966 AN: 152136 Hom.: 6804 Cov.: 32 AF XY: 0.282 AC XY: 20947 AN XY: 74376

African (AFR) AF: 0.154 AC: 6383 AN: 41514

American (AMR) AF: 0.254 AC: 3883 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 697 AN: 3468

East Asian (EAS) AF: 0.674 AC: 3473 AN: 5150

South Asian (SAS) AF: 0.302 AC: 1456 AN: 4824

European-Finnish (FIN) AF: 0.440 AC: 4658 AN: 10584

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20729 AN: 67994

Other (OTH) AF: 0.256 AC: 542 AN: 2114

Alfa AF: 0.288 Hom.: 24480

Bravo AF: 0.256

Asia WGS AF: 0.456 AC: 1580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.88
DANN	Benign	0.48
PhyloP100		-0.86
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: rs11198856; hg19: chr10-121041698;