Variant chr9-69012838-G-GGC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_002732.4(PRKACG):c.*198_*199insGC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.25 ( 4979 hom., cov: 20)

Exomes 𝑓: 0.22 ( 11222 hom. )

Consequence

PRKACG
NM_002732.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.279

Variant links:

Genes affected

PRKACG (HGNC:9382): (protein kinase cAMP-activated catalytic subunit gamma) Cyclic AMP-dependent protein kinase (PKA) consists of two catalytic subunits and a regulatory subunit dimer. This gene encodes the gamma form of its catalytic subunit. The gene is intronless and is thought to be a retrotransposon derived from the gene for the alpha form of the PKA catalytic subunit. [provided by RefSeq, Jul 2008]

PRKACG links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 9-69012838-G-GGC is Benign according to our data. Variant chr9-69012838-G-GGC is described in ClinVar as [Benign]. Clinvar id is 1269471.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRKACG	NM_002732.4 linkuse as main transcript	c.198_199insGC		3_prime_UTR_variant	1/1	ENST00000377276.5	NP_002723.2	P22612

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRKACG	ENST00000377276.5 linkuse as main transcript	c.198_199insGC		3_prime_UTR_variant	1/1	6	NM_002732.4	ENSP00000366488.2		P22612

Frequencies

GnomAD3 genomes

AF:

0.247

AC:

37325

AN:

150990

Hom.:

4965

Cov.:

show subpopulations

Gnomad AFR

AF:

0.304

Gnomad AMI

AF:

0.340

Gnomad AMR

AF:

0.332

Gnomad ASJ

AF:

0.220

Gnomad EAS

AF:

0.0419

Gnomad SAS

AF:

0.201

Gnomad FIN

AF:

0.173

Gnomad MID

AF:

0.264

Gnomad NFE

AF:

0.224

Gnomad OTH

AF:

0.257

GnomAD4 exome

AF:

0.215

AC:

94073

AN:

437492

Hom.:

11222

Cov.:

AF XY:

0.213

AC XY:

49001

AN XY:

229614

show subpopulations

Gnomad4 AFR exome

AF:

0.309

Gnomad4 AMR exome

AF:

0.351

Gnomad4 ASJ exome

AF:

0.230

Gnomad4 EAS exome

AF:

0.0316

Gnomad4 SAS exome

AF:

0.207

Gnomad4 FIN exome

AF:

0.185

Gnomad4 NFE exome

AF:

0.224

Gnomad4 OTH exome

AF:

0.237

GnomAD4 genome

AF:

0.247

AC:

37395

AN:

151110

Hom.:

4979

Cov.:

AF XY:

0.243

AC XY:

17921

AN XY:

73780

show subpopulations

Gnomad4 AFR

AF:

0.304

Gnomad4 AMR

AF:

0.332

Gnomad4 ASJ

AF:

0.220

Gnomad4 EAS

AF:

0.0420

Gnomad4 SAS

AF:

0.202

Gnomad4 FIN

AF:

0.173

Gnomad4 NFE

AF:

0.224

Gnomad4 OTH

AF:

0.256

Alfa

AF:

0.0656

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over