rs2593595
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000151.4(G6PC1):c.340+188A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 602,622 control chromosomes in the GnomAD database, including 32,689 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.38 ( 17381 hom., cov: 31)
Exomes 𝑓: 0.23 ( 15308 hom. )
Consequence
G6PC1
NM_000151.4 intron
NM_000151.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.871
Genes affected
G6PC1 (HGNC:4056): (glucose-6-phosphatase catalytic subunit 1) Glucose-6-phosphatase (G6Pase) is a multi-subunit integral membrane protein of the endoplasmic reticulum that is composed of a catalytic subunit and transporters for G6P, inorganic phosphate, and glucose. This gene (G6PC) is one of the three glucose-6-phosphatase catalytic-subunit-encoding genes in human: G6PC, G6PC2 and G6PC3. Glucose-6-phosphatase catalyzes the hydrolysis of D-glucose 6-phosphate to D-glucose and orthophosphate and is a key enzyme in glucose homeostasis, functioning in gluconeogenesis and glycogenolysis. Mutations in this gene cause glycogen storage disease type I (GSD1). This disease, also known as von Gierke disease, is a metabolic disorder characterized by severe hypoglycemia associated with the accumulation of glycogen and fat in the liver and kidneys.[provided by RefSeq, Feb 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 17-42904228-A-G is Benign according to our data. Variant chr17-42904228-A-G is described in ClinVar as [Benign]. Clinvar id is 1238046.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
G6PC1 | NM_000151.4 | c.340+188A>G | intron_variant | ENST00000253801.7 | |||
G6PC1 | NM_001270397.2 | c.340+188A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
G6PC1 | ENST00000253801.7 | c.340+188A>G | intron_variant | 1 | NM_000151.4 | P1 | |||
G6PC1 | ENST00000585489.1 | c.340+188A>G | intron_variant | 5 | |||||
G6PC1 | ENST00000592383.5 | c.340+188A>G | intron_variant | 2 | |||||
G6PC1 | ENST00000588481.1 | n.593A>G | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.383 AC: 58158AN: 151984Hom.: 17314 Cov.: 31
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GnomAD4 exome AF: 0.230 AC: 103502AN: 450520Hom.: 15308 Cov.: 4 AF XY: 0.232 AC XY: 56358AN XY: 242578
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GnomAD4 genome ? AF: 0.383 AC: 58286AN: 152102Hom.: 17381 Cov.: 31 AF XY: 0.381 AC XY: 28304AN XY: 74354
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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 | GeneDx | May 11, 2021 | - - |
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