10-52013039-T-C

Position:

• chr10-52013039-T-C

Variant summary

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

The NM_006258.4(PRKG1):​c.763-41445T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 152,088 control chromosomes in the GnomAD database, including 42,429 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 0.74 (42429 hom., cov: 32)
• Consequence: PRKG1 NM_006258.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.620

Genes affected

PRKG1 (HGNC:9414): (protein kinase cGMP-dependent 1) Mammals have three different isoforms of cyclic GMP-dependent protein kinase (Ialpha, Ibeta, and II). These PRKG isoforms act as key mediators of the nitric oxide/cGMP signaling pathway and are important components of many signal transduction processes in diverse cell types. This PRKG1 gene on human chromosome 10 encodes the soluble Ialpha and Ibeta isoforms of PRKG by alternative transcript splicing. A separate gene on human chromosome 4, PRKG2, encodes the membrane-bound PRKG isoform II. The PRKG1 proteins play a central role in regulating cardiovascular and neuronal functions in addition to relaxing smooth muscle tone, preventing platelet aggregation, and modulating cell growth. This gene is most strongly expressed in all types of smooth muscle, platelets, cerebellar Purkinje cells, hippocampal neurons, and the lateral amygdala. Isoforms Ialpha and Ibeta have identical cGMP-binding and catalytic domains but differ in their leucine/isoleucine zipper and autoinhibitory sequences and therefore differ in their dimerization substrates and kinase enzyme activity. [provided by RefSeq, Sep 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRKG1	NM_006258.4	c.763-41445T>C		intron_variant		ENST00000373980.11	NP_006249.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRKG1	ENST00000373980.11	c.763-41445T>C		intron_variant		1	NM_006258.4	ENSP00000363092
PRKG1	ENST00000373976.9	c.763-41445T>C		intron_variant		3		ENSP00000363087
PRKG1	ENST00000401604.8	c.718-41445T>C		intron_variant		5		ENSP00000384200	P1
PRKG1	ENST00000645324.1	c.763-41445T>C		intron_variant				ENSP00000494124

Frequencies

GnomAD3 genomes AF: 0.744 AC: 113092 AN: 151970 Hom.: 42408 Cov.: 32

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.744 AC: 113170 AN: 152088 Hom.: 42429 Cov.: 32 AF XY: 0.740 AC XY: 55003 AN XY: 74326

Gnomad4 AFR AF: 0.807

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.709

Gnomad4 EAS AF: 0.733

Gnomad4 SAS AF: 0.749

Gnomad4 FIN AF: 0.653

Gnomad4 NFE AF: 0.736

Gnomad4 OTH AF: 0.755

Alfa AF: 0.724 Hom.: 15582

Bravo AF: 0.745

Asia WGS AF: 0.760 AC: 2644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.44

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: rs7893146; hg19: chr10-53772799;