1-147158337-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005399.5(PRKAB2):​c.*1228G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,886 control chromosomes in the GnomAD database, including 18,336 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 0.48 ( 18336 hom., cov: 31)
Exomes 𝑓: 0.50 ( 0 hom. )

Consequence

PRKAB2
NM_005399.5 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.82
Variant links:
Genes affected
PRKAB2 (HGNC:9379): (protein kinase AMP-activated non-catalytic subunit beta 2) The protein encoded by this gene is a regulatory 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. This subunit may be a positive regulator of AMPK activity. It is highly expressed in skeletal muscle and thus may have tissue-specific roles. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2013]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PRKAB2NM_005399.5 linkuse as main transcriptc.*1228G>A 3_prime_UTR_variant 8/8 ENST00000254101.4 NP_005390.1 O43741-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PRKAB2ENST00000254101.4 linkuse as main transcriptc.*1228G>A 3_prime_UTR_variant 8/81 NM_005399.5 ENSP00000254101.3 O43741-1

Frequencies

GnomAD3 genomes
AF:
0.476
AC:
72174
AN:
151764
Hom.:
18307
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.578
Gnomad AMI
AF:
0.388
Gnomad AMR
AF:
0.530
Gnomad ASJ
AF:
0.360
Gnomad EAS
AF:
0.858
Gnomad SAS
AF:
0.558
Gnomad FIN
AF:
0.479
Gnomad MID
AF:
0.513
Gnomad NFE
AF:
0.373
Gnomad OTH
AF:
0.457
GnomAD4 exome
AF:
0.500
AC:
1
AN:
2
Hom.:
0
Cov.:
0
AF XY:
0.500
AC XY:
1
AN XY:
2
show subpopulations
Gnomad4 OTH exome
AF:
0.500
GnomAD4 genome
AF:
0.476
AC:
72259
AN:
151884
Hom.:
18336
Cov.:
31
AF XY:
0.485
AC XY:
36014
AN XY:
74232
show subpopulations
Gnomad4 AFR
AF:
0.578
Gnomad4 AMR
AF:
0.531
Gnomad4 ASJ
AF:
0.360
Gnomad4 EAS
AF:
0.858
Gnomad4 SAS
AF:
0.557
Gnomad4 FIN
AF:
0.479
Gnomad4 NFE
AF:
0.373
Gnomad4 OTH
AF:
0.462
Alfa
AF:
0.405
Hom.:
19452
Bravo
AF:
0.483
Asia WGS
AF:
0.678
AC:
2358
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
CADD
Benign
9.0
DANN
Benign
0.74

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

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

Other links and lift over

dbSNP: rs10900321; hg19: chr1-146629916; API