2-27496946-G-A
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001486.4(GCKR):c.42G>A(p.Pro14=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000291 in 1,613,394 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: 𝑓 0.000085 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000023 ( 0 hom. )
Consequence
GCKR
NM_001486.4 synonymous
NM_001486.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.98
Genes affected
GCKR (HGNC:4196): (glucokinase regulator) This gene encodes a protein belonging to the GCKR subfamily of the SIS (Sugar ISomerase) family of proteins. The gene product is a regulatory protein that inhibits glucokinase in liver and pancreatic islet cells by binding non-covalently to form an inactive complex with the enzyme. This gene is considered a susceptibility gene candidate for a form of maturity-onset diabetes of the young (MODY). [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BP6
Variant 2-27496946-G-A is Benign according to our data. Variant chr2-27496946-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2190904.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.98 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GCKR | NM_001486.4 | c.42G>A | p.Pro14= | synonymous_variant | 1/19 | ENST00000264717.7 | |
GCKR | XM_011532763.1 | c.42G>A | p.Pro14= | synonymous_variant | 1/13 | ||
GCKR | XR_001738699.1 | n.108G>A | non_coding_transcript_exon_variant | 1/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GCKR | ENST00000264717.7 | c.42G>A | p.Pro14= | synonymous_variant | 1/19 | 1 | NM_001486.4 | P1 | |
GCKR | ENST00000472290.1 | n.64G>A | non_coding_transcript_exon_variant | 1/11 | 1 | ||||
GCKR | ENST00000417872.5 | n.99G>A | non_coding_transcript_exon_variant | 1/7 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152142Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251436Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135898
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GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461252Hom.: 0 Cov.: 30 AF XY: 0.0000248 AC XY: 18AN XY: 727008
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GnomAD4 genome AF: 0.0000854 AC: 13AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74308
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 21, 2023 | - - |
Computational scores
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Benign
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DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at