7-151556171-AC-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1BS2
The NM_016203.4(PRKAG2):c.*1029delG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000327 in 113,000 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00033 ( 0 hom., cov: 30)
Consequence
PRKAG2
NM_016203.4 3_prime_UTR
NM_016203.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.358
Publications
0 publications found
Genes affected
PRKAG2 (HGNC:9386): (protein kinase AMP-activated non-catalytic subunit gamma 2) AMP-activated protein kinase (AMPK) is a heterotrimeric protein composed of a catalytic alpha subunit, a noncatalytic beta subunit, and a noncatalytic regulatory gamma subunit. Various forms of each of these subunits exist, encoded by different genes. AMPK is an important energy-sensing enzyme that monitors cellular energy status and functions by inactivating key enzymes involved in regulating de novo biosynthesis of fatty acid and cholesterol. This gene is a member of the AMPK gamma subunit family. Mutations in this gene have been associated with Wolff-Parkinson-White syndrome, familial hypertrophic cardiomyopathy, and glycogen storage disease of the heart. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jan 2015]
PRKAG2 Gene-Disease associations (from GenCC):
- hypertrophic cardiomyopathyInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- hypertrophic cardiomyopathy 6Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, PanelApp Australia, Labcorp Genetics (formerly Invitae)
- PRKAG2-related cardiomyopathyInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- lethal congenital glycogen storage disease of heartInheritance: AD Classification: STRONG Submitted by: PanelApp Australia, Genomics England PanelApp
- Wolff-Parkinson-White syndromeInheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -8 ACMG points.
BS1
Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.000327 (37/113000) while in subpopulation AFR AF = 0.000836 (30/35872). AF 95% confidence interval is 0.000601. There are 0 homozygotes in GnomAd4. There are 19 alleles in the male GnomAd4 subpopulation. Median coverage is 30. This position passed quality control check.
BS2
High AC in GnomAd4 at 37 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRKAG2 | NM_016203.4 | c.*1029delG | 3_prime_UTR_variant | Exon 16 of 16 | ENST00000287878.9 | NP_057287.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000328 AC: 37AN: 112922Hom.: 0 Cov.: 30 show subpopulations
GnomAD3 genomes
AF:
AC:
37
AN:
112922
Hom.:
Cov.:
30
Gnomad AFR
AF:
Gnomad AMI
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Gnomad ASJ
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Gnomad EAS
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GnomAD4 exome Cov.: 0
GnomAD4 exome
Cov.:
0
GnomAD4 genome AF: 0.000327 AC: 37AN: 113000Hom.: 0 Cov.: 30 AF XY: 0.000352 AC XY: 19AN XY: 53914 show subpopulations
GnomAD4 genome
AF:
AC:
37
AN:
113000
Hom.:
Cov.:
30
AF XY:
AC XY:
19
AN XY:
53914
show subpopulations
African (AFR)
AF:
AC:
30
AN:
35872
American (AMR)
AF:
AC:
6
AN:
11158
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2560
East Asian (EAS)
AF:
AC:
0
AN:
3952
South Asian (SAS)
AF:
AC:
0
AN:
3124
European-Finnish (FIN)
AF:
AC:
0
AN:
4930
Middle Eastern (MID)
AF:
AC:
0
AN:
222
European-Non Finnish (NFE)
AF:
AC:
0
AN:
48872
Other (OTH)
AF:
AC:
1
AN:
1490
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.491
Heterozygous variant carriers
0
1
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4
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0.20
0.40
0.60
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0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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