rs2302531
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_016203.4(PRKAG2):c.1052-42C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 1,577,214 control chromosomes in the GnomAD database, including 13,342 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.11 ( 1123 hom., cov: 33)
Exomes 𝑓: 0.12 ( 12219 hom. )
Consequence
PRKAG2
NM_016203.4 intron
NM_016203.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.757
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
?
Variant 7-151570267-G-A is Benign according to our data. Variant chr7-151570267-G-A is described in ClinVar as [Benign]. Clinvar id is 260694.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRKAG2 | NM_016203.4 | c.1052-42C>T | intron_variant | ENST00000287878.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKAG2 | ENST00000287878.9 | c.1052-42C>T | intron_variant | 1 | NM_016203.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.106 AC: 16061AN: 152046Hom.: 1119 Cov.: 33
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GnomAD3 exomes AF: 0.148 AC: 36287AN: 245054Hom.: 3308 AF XY: 0.149 AC XY: 19787AN XY: 132714
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GnomAD4 exome AF: 0.122 AC: 173407AN: 1425050Hom.: 12219 Cov.: 29 AF XY: 0.125 AC XY: 88296AN XY: 708664
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GnomAD4 genome ? AF: 0.106 AC: 16063AN: 152164Hom.: 1123 Cov.: 33 AF XY: 0.109 AC XY: 8113AN XY: 74374
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at