rs369055649
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6BP7
The NM_001244710.2(GFPT1):c.1629C>T(p.Asp543=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000453 in 1,610,044 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000029 ( 0 hom. )
Consequence
GFPT1
NM_001244710.2 synonymous
NM_001244710.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0850
Genes affected
GFPT1 (HGNC:4241): (glutamine--fructose-6-phosphate transaminase 1) This gene encodes the first and rate-limiting enzyme of the hexosamine pathway and controls the flux of glucose into the hexosamine pathway. The product of this gene catalyzes the formation of glucosamine 6-phosphate. [provided by RefSeq, Sep 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
Variant 2-69329393-G-A is Benign according to our data. Variant chr2-69329393-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 435320.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1}.
BP7
Synonymous conserved (PhyloP=-0.085 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GFPT1 | NM_001244710.2 | c.1629C>T | p.Asp543= | synonymous_variant | 17/20 | ENST00000357308.9 | |
GFPT1 | NM_002056.4 | c.1575C>T | p.Asp525= | synonymous_variant | 16/19 | ||
GFPT1 | XM_017003801.2 | c.1704C>T | p.Asp568= | synonymous_variant | 17/20 | ||
GFPT1 | XM_017003802.3 | c.1650C>T | p.Asp550= | synonymous_variant | 16/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GFPT1 | ENST00000357308.9 | c.1629C>T | p.Asp543= | synonymous_variant | 17/20 | 5 | NM_001244710.2 | ||
GFPT1 | ENST00000361060.5 | c.1575C>T | p.Asp525= | synonymous_variant | 16/19 | 1 | P1 | ||
GFPT1 | ENST00000674507.1 | c.1575C>T | p.Asp525= | synonymous_variant | 16/18 | ||||
GFPT1 | ENST00000674438.1 | c.1359C>T | p.Asp453= | synonymous_variant | 14/17 |
Frequencies
GnomAD3 genomes AF: 0.000204 AC: 31AN: 152122Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000677 AC: 17AN: 251146Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135736
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GnomAD4 exome AF: 0.0000288 AC: 42AN: 1457804Hom.: 0 Cov.: 29 AF XY: 0.0000262 AC XY: 19AN XY: 725470
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GnomAD4 genome AF: 0.000204 AC: 31AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74452
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 11, 2015 | - - |
Congenital myasthenic syndrome 12 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 17, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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