3-141794181-T-C

Variant names:

• chr3-141794181-T-C
• rs9831276
• NM_139209.3:c.1050+13370T>C

Variant summary

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

The NM_139209.3(GRK7):​c.1050+13370T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.81 in 152,204 control chromosomes in the GnomAD database, including 50,680 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 0.81 (50680 hom., cov: 33)
• Consequence: GRK7 NM_139209.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.520
• Publications: 4 publications found

Genes affected

GRK7 (HGNC:17031): (G protein-coupled receptor kinase 7) This gene encodes a member of the guanine nucleotide-binding protein (G protein)-coupled receptor kinase subfamily of the Ser/Thr protein kinase family. It is specifically expressed in the retina and the encoded protein has been shown to phosphorylate cone opsins and initiate their deactivation. [provided by RefSeq, Jul 2008]

ENSG00000285558 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GRK7	NM_139209.3	c.1050+13370T>C		intron_variant	Intron 4 of 5	ENST00000682958.1	NP_631948.1
GRK7	XM_047447449.1	c.1050+13370T>C		intron_variant	Intron 5 of 6		XP_047303405.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRK7	ENST00000682958.1	c.1050+13370T>C		intron_variant	Intron 4 of 5		NM_139209.3	ENSP00000508022.1
GRK7	ENST00000264952.2	c.1050+13370T>C		intron_variant	Intron 2 of 3	1		ENSP00000264952.2
ENSG00000285558	ENST00000648835.1	n.*391+13370T>C		intron_variant	Intron 2 of 2			ENSP00000498049.1

Frequencies

GnomAD3 genomes AF: 0.810 AC: 123189 AN: 152086 Hom.: 50623 Cov.: 33

Gnomad AFR AF: 0.956

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.751

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.810 AC: 123304 AN: 152204 Hom.: 50680 Cov.: 33 AF XY: 0.806 AC XY: 59994 AN XY: 74402

African (AFR) AF: 0.956 AC: 39704 AN: 41546

American (AMR) AF: 0.802 AC: 12262 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.751 AC: 2605 AN: 3470

East Asian (EAS) AF: 0.744 AC: 3852 AN: 5176

South Asian (SAS) AF: 0.770 AC: 3709 AN: 4818

European-Finnish (FIN) AF: 0.683 AC: 7231 AN: 10588

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.753 AC: 51213 AN: 67996

Other (OTH) AF: 0.812 AC: 1714 AN: 2110

Alfa AF: 0.788 Hom.: 8362

Bravo AF: 0.824

Asia WGS AF: 0.788 AC: 2739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.2
DANN	Benign	0.62
PhyloP100		0.52
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: rs9831276; hg19: chr3-141513023;