rs10508965

chr10-52209518-G-Achr10-52209518-G-T

Variant summary

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

The NM_006258.4(PRKG1):c.1077-42052G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0862 in 152,120 control chromosomes in the GnomAD database, including 1,109 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 0.086 (1109 hom., cov: 32)
• Consequence: PRKG1 NM_006258.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410

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]

LOC124902425 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRKG1	NM_006258.4	c.1077-42052G>A		intron_variant		ENST00000373980.11
LOC124902425	XR_007062145.1	n.148-11799C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRKG1	ENST00000373980.11	c.1077-42052G>A		intron_variant		1	NM_006258.4
PRKG1	ENST00000401604.8	c.1032-42052G>A		intron_variant		5		P1
PRKG1	ENST00000672084.1	c.228-42052G>A		intron_variant
PRKG1	ENST00000373975.3	n.436-42052G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0862 AC: 13096 AN: 152002 Hom.: 1108 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0718

Gnomad ASJ AF: 0.0721

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0338

Gnomad FIN AF: 0.00915

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0319

Gnomad OTH AF: 0.0852

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

GnomAD4 genome AF: 0.0862 AC: 13114 AN: 152120 Hom.: 1109 Cov.: 32 AF XY: 0.0838 AC XY: 6231 AN XY: 74356

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.0716

Gnomad4 ASJ AF: 0.0721

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0336

Gnomad4 FIN AF: 0.00915

Gnomad4 NFE AF: 0.0319

Gnomad4 OTH AF: 0.0843

Alfa AF: 0.0105 Hom.: 6

Bravo AF: 0.0964

Asia WGS AF: 0.0270 AC: 97 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	1.5
Dann	Benign	0.48

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: rs10508965; hg19: chr10-53969278;