chr2-162144091-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002054.5(GCG):c.472A>G(p.Ile158Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00251 in 1,612,636 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0022 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0026 ( 18 hom. )
Consequence
GCG
NM_002054.5 missense
NM_002054.5 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: 0.270
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 -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.005893886).
BP6
?
Variant 2-162144091-T-C is Benign according to our data. Variant chr2-162144091-T-C is described in ClinVar as [Benign]. Clinvar id is 718683.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAdExome at 3 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GCG | NM_002054.5 | c.472A>G | p.Ile158Val | missense_variant | 5/6 | ENST00000418842.7 | |
LOC101929532 | NR_110255.1 | n.93-17679T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GCG | ENST00000418842.7 | c.472A>G | p.Ile158Val | missense_variant | 5/6 | 1 | NM_002054.5 | P1 | |
GCG | ENST00000375497.3 | c.472A>G | p.Ile158Val | missense_variant | 5/6 | 5 | P1 | ||
GCG | ENST00000483769.1 | n.325A>G | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00216 AC: 329AN: 152194Hom.: 1 Cov.: 32
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?
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GnomAD3 exomes AF: 0.00268 AC: 667AN: 248640Hom.: 3 AF XY: 0.00290 AC XY: 391AN XY: 134870
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GnomAD4 exome AF: 0.00255 AC: 3724AN: 1460324Hom.: 18 Cov.: 29 AF XY: 0.00266 AC XY: 1932AN XY: 726546
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GnomAD4 genome ? AF: 0.00215 AC: 328AN: 152312Hom.: 1 Cov.: 32 AF XY: 0.00255 AC XY: 190AN XY: 74480
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342
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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 | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N
MutationTaster
Benign
N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;B
Vest4
MVP
MPC
ClinPred
T
GERP RS
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gMVP
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