5-40769460-A-G
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_006251.6(PRKAA1):āc.552T>Cā(p.Ser184=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000141 in 1,611,510 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.00068 ( 0 hom., cov: 32)
Exomes š: 0.000085 ( 0 hom. )
Consequence
PRKAA1
NM_006251.6 synonymous
NM_006251.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.913
Genes affected
PRKAA1 (HGNC:9376): (protein kinase AMP-activated catalytic subunit alpha 1) The protein encoded by this gene belongs to the ser/thr protein kinase family. It is the catalytic subunit of the 5'-prime-AMP-activated protein kinase (AMPK). AMPK is a cellular energy sensor conserved in all eukaryotic cells. The kinase activity of AMPK is activated by the stimuli that increase the cellular AMP/ATP ratio. AMPK regulates the activities of a number of key metabolic enzymes through phosphorylation. It protects cells from stresses that cause ATP depletion by switching off ATP-consuming biosynthetic pathways. Alternatively spliced transcript variants encoding distinct isoforms have been observed. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BP6
Variant 5-40769460-A-G is Benign according to our data. Variant chr5-40769460-A-G is described in ClinVar as [Benign]. Clinvar id is 731718.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.913 with no splicing effect.
BS2
High AC in GnomAd4 at 103 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRKAA1 | NM_006251.6 | c.552T>C | p.Ser184= | synonymous_variant | 5/9 | ENST00000397128.7 | NP_006242.5 | |
LOC124900968 | XR_007058747.1 | n.1451+4993A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRKAA1 | ENST00000397128.7 | c.552T>C | p.Ser184= | synonymous_variant | 5/9 | 1 | NM_006251.6 | ENSP00000380317 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000677 AC: 103AN: 152198Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000194 AC: 48AN: 247732Hom.: 0 AF XY: 0.000134 AC XY: 18AN XY: 134486
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GnomAD4 exome AF: 0.0000850 AC: 124AN: 1459194Hom.: 0 Cov.: 30 AF XY: 0.0000620 AC XY: 45AN XY: 725934
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GnomAD4 genome AF: 0.000676 AC: 103AN: 152316Hom.: 0 Cov.: 32 AF XY: 0.000671 AC XY: 50AN XY: 74480
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Jun 10, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at