rs884970

Variant names:

• chr10-119364989-A-G
• rs884970
• NM_005308.3:c.149-15826A>G

Your query was ambiguous. Multiple possible variants found:

• chr10-119364989-A-G
• chr10-119364989-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.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
• Publications: 4 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=-0.88).
• 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 rank	MANE	Protein	UniProt
GRK5	NM_005308.3	c.149-15826A>G		intron_variant	Intron 2 of 15	ENST00000392870.3	NP_005299.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRK5	ENST00000392870.3	c.149-15826A>G		intron_variant	Intron 2 of 15	1	NM_005308.3	ENSP00000376609.2

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

African (AFR) AF: 0.295 AC: 12219 AN: 41430

American (AMR) AF: 0.546 AC: 8331 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2124 AN: 3466

East Asian (EAS) AF: 0.320 AC: 1655 AN: 5178

South Asian (SAS) AF: 0.438 AC: 2104 AN: 4804

European-Finnish (FIN) AF: 0.574 AC: 6052 AN: 10552

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.540 AC: 36690 AN: 67956

Other (OTH) AF: 0.497 AC: 1049 AN: 2110

Alfa AF: 0.503 Hom.: 35385

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
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: rs884970; hg19: chr10-121124501;