chr16-30748827-C-T
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_000294.3(PHKG2):c.7C>T(p.Leu3=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000429 in 1,399,282 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 Likely benign (★).
Frequency
Genomes: not found (cov: 30)
Exomes 𝑓: 0.0000043 ( 0 hom. )
Consequence
PHKG2
NM_000294.3 synonymous
NM_000294.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.75
Genes affected
PHKG2 (HGNC:8931): (phosphorylase kinase catalytic subunit gamma 2) Phosphorylase kinase is a polymer of 16 subunits, four each of alpha, beta, gamma and delta. The alpha subunit includes the skeletal muscle and hepatic isoforms, encoded by two different genes. The beta subunit is the same in both the muscle and hepatic isoforms, and encoded by one gene. The gamma subunit also includes the skeletal muscle and hepatic isoforms, and the hepatic isoform is encoded by this gene. The delta subunit is a calmodulin and can be encoded by three different genes. The gamma subunits contain the active site of the enzyme, whereas the alpha and beta subunits have regulatory functions controlled by phosphorylation. The delta subunit mediates the dependence of the enzyme on calcium concentration. Mutations in this gene cause glycogen storage disease type 9C, also known as autosomal liver glycogenosis. Alternatively spliced transcript variants encoding different isoforms have been identified in this gene.[provided by RefSeq, Feb 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BP6
Variant 16-30748827-C-T is Benign according to our data. Variant chr16-30748827-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2971621.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.75 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PHKG2 | NM_000294.3 | c.7C>T | p.Leu3= | synonymous_variant | 2/10 | ENST00000563588.6 | NP_000285.1 | |
PHKG2 | NM_001172432.2 | c.7C>T | p.Leu3= | synonymous_variant | 2/11 | NP_001165903.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PHKG2 | ENST00000563588.6 | c.7C>T | p.Leu3= | synonymous_variant | 2/10 | 1 | NM_000294.3 | ENSP00000455607 | P4 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD3 genomes
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30
GnomAD3 exomes AF: 0.00000641 AC: 1AN: 156112Hom.: 0 AF XY: 0.0000121 AC XY: 1AN XY: 82664
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GnomAD4 exome AF: 0.00000429 AC: 6AN: 1399282Hom.: 0 Cov.: 32 AF XY: 0.00000579 AC XY: 4AN XY: 690254
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GnomAD4 genome Cov.: 30
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Glycogen storage disease IXc Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 10, 2023 | - - |
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