rs7581952
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000418842.7(GCG):c.393-176T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0323 in 585,722 control chromosomes in the GnomAD database, including 1,328 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.037 ( 479 hom., cov: 32)
Exomes 𝑓: 0.031 ( 849 hom. )
Consequence
GCG
ENST00000418842.7 intron
ENST00000418842.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.146
Genes affected
GCG (HGNC:4191): (glucagon) The protein encoded by this gene is actually a preproprotein that is cleaved into four distinct mature peptides. One of these, glucagon, is a pancreatic hormone that counteracts the glucose-lowering action of insulin by stimulating glycogenolysis and gluconeogenesis. Glucagon is a ligand for a specific G-protein linked receptor whose signalling pathway controls cell proliferation. Two of the other peptides are secreted from gut endocrine cells and promote nutrient absorption through distinct mechanisms. Finally, the fourth peptide is similar to glicentin, an active enteroglucagon. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GCG | NM_002054.5 | c.393-176T>G | intron_variant | ENST00000418842.7 | NP_002045.1 | |||
LOC101929532 | NR_110255.1 | n.93-17424A>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GCG | ENST00000418842.7 | c.393-176T>G | intron_variant | 1 | NM_002054.5 | ENSP00000387662 | P1 | |||
GCG | ENST00000375497.3 | c.393-176T>G | intron_variant | 5 | ENSP00000364647 | P1 | ||||
GCG | ENST00000483769.1 | n.70T>G | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0370 AC: 5637AN: 152174Hom.: 470 Cov.: 32
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GnomAD4 exome AF: 0.0305 AC: 13237AN: 433430Hom.: 849 Cov.: 4 AF XY: 0.0288 AC XY: 6602AN XY: 228892
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GnomAD4 genome AF: 0.0372 AC: 5668AN: 152292Hom.: 479 Cov.: 32 AF XY: 0.0393 AC XY: 2929AN XY: 74464
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at