rs10789038

Positions:

• chr1-56651444-A-G

Variant summary

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

The NM_006252.4(PRKAA2):​c.94+5963A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,952 control chromosomes in the GnomAD database, including 14,968 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 0.44 (14968 hom., cov: 31)
• Consequence: PRKAA2 NM_006252.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377

Genes affected

PRKAA2 (HGNC:9377): (protein kinase AMP-activated catalytic subunit alpha 2) The protein encoded by this gene is a catalytic subunit of the AMP-activated protein kinase (AMPK). AMPK is a heterotrimer consisting of an alpha catalytic subunit, and non-catalytic beta and gamma subunits. AMPK is an important energy-sensing enzyme that monitors cellular energy status. In response to cellular metabolic stresses, AMPK is activated, and thus phosphorylates and inactivates acetyl-CoA carboxylase (ACC) and beta-hydroxy beta-methylglutaryl-CoA reductase (HMGCR), key enzymes involved in regulating de novo biosynthesis of fatty acid and cholesterol. Studies of the mouse counterpart suggest that this catalytic subunit may control whole-body insulin sensitivity and is necessary for maintaining myocardial energy homeostasis during ischemia. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRKAA2	NM_006252.4	c.94+5963A>G		intron_variant		ENST00000371244.9
PRKAA2	XM_017001693.2	c.-177+5449A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRKAA2	ENST00000371244.9	c.94+5963A>G		intron_variant		1	NM_006252.4	P1

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66109 AN: 151830 Hom.: 14963 Cov.: 31

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.435 AC: 66132 AN: 151952 Hom.: 14968 Cov.: 31 AF XY: 0.427 AC XY: 31694 AN XY: 74230

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.443

Alfa AF: 0.466 Hom.: 4640

Bravo AF: 0.428

Asia WGS AF: 0.226 AC: 788 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.79

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: rs10789038; hg19: chr1-57117117; COSMIC: COSV64802838;