9-94606869-G-A
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Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_000507.4(FBP1):c.651C>T(p.Ala217=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 1,613,350 control chromosomes in the GnomAD database, including 93,705 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.31 ( 7599 hom., cov: 32)
Exomes 𝑓: 0.34 ( 86106 hom. )
Consequence
FBP1
NM_000507.4 synonymous
NM_000507.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.19
Genes affected
FBP1 (HGNC:3606): (fructose-bisphosphatase 1) Fructose-1,6-bisphosphatase 1, a gluconeogenesis regulatory enzyme, catalyzes the hydrolysis of fructose 1,6-bisphosphate to fructose 6-phosphate and inorganic phosphate. Fructose-1,6-diphosphatase deficiency is associated with hypoglycemia and metabolic acidosis. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -19 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP6
Variant 9-94606869-G-A is Benign according to our data. Variant chr9-94606869-G-A is described in ClinVar as [Benign]. Clinvar id is 256322.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-94606869-G-A is described in Lovd as [Benign].
BP7
Synonymous conserved (PhyloP=2.19 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FBP1 | NM_000507.4 | c.651C>T | p.Ala217= | synonymous_variant | 5/7 | ENST00000375326.9 | |
FBP1 | NM_001127628.2 | c.651C>T | p.Ala217= | synonymous_variant | 6/8 | ||
FBP1 | XM_006717005.5 | c.405C>T | p.Ala135= | synonymous_variant | 5/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FBP1 | ENST00000375326.9 | c.651C>T | p.Ala217= | synonymous_variant | 5/7 | 1 | NM_000507.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.313 AC: 47624AN: 152056Hom.: 7592 Cov.: 32
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GnomAD3 exomes AF: 0.329 AC: 82659AN: 251338Hom.: 14801 AF XY: 0.333 AC XY: 45206AN XY: 135844
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GnomAD4 exome AF: 0.338 AC: 493510AN: 1461176Hom.: 86106 Cov.: 38 AF XY: 0.339 AC XY: 246236AN XY: 726936
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GnomAD4 genome AF: 0.313 AC: 47671AN: 152174Hom.: 7599 Cov.: 32 AF XY: 0.313 AC XY: 23273AN XY: 74376
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ClinVar
Significance: Benign
Submissions summary: Benign:7
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:3
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 30, 2012 | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Fructose-biphosphatase deficiency Benign:3
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 10, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
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BayesDel_noAF
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DANN
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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