rs1064891
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004566.4(PFKFB3):c.*1669T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 151,876 control chromosomes in the GnomAD database, including 11,094 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 0.37 ( 11089 hom., cov: 30)
Exomes 𝑓: 0.33 ( 5 hom. )
Consequence
PFKFB3
NM_004566.4 3_prime_UTR
NM_004566.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.105
Genes affected
PFKFB3 (HGNC:8874): (6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3) The protein encoded by this gene belongs to a family of bifunctional proteins that are involved in both the synthesis and degradation of fructose-2,6-bisphosphate, a regulatory molecule that controls glycolysis in eukaryotes. The encoded protein has a 6-phosphofructo-2-kinase activity that catalyzes the synthesis of fructose-2,6-bisphosphate (F2,6BP), and a fructose-2,6-biphosphatase activity that catalyzes the degradation of F2,6BP. This protein is required for cell cycle progression and prevention of apoptosis. It functions as a regulator of cyclin-dependent kinase 1, linking glucose metabolism to cell proliferation and survival in tumor cells. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2016]
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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=-0.83).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PFKFB3 | NM_004566.4 | c.*1669T>C | 3_prime_UTR_variant | 15/15 | ENST00000379775.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PFKFB3 | ENST00000379775.9 | c.*1669T>C | 3_prime_UTR_variant | 15/15 | 1 | NM_004566.4 | |||
PFKFB3 | ENST00000379789.8 | c.*1669T>C | 3_prime_UTR_variant | 15/15 | 1 | ||||
PFKFB3 | ENST00000360521.7 | c.*1710T>C | 3_prime_UTR_variant | 16/16 | 5 | P4 | |||
PFKFB3 | ENST00000640683.1 | c.1515+8246T>C | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.374 AC: 56639AN: 151632Hom.: 11081 Cov.: 30
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GnomAD4 exome AF: 0.333 AC: 42AN: 126Hom.: 5 Cov.: 0 AF XY: 0.319 AC XY: 23AN XY: 72
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GnomAD4 genome ? AF: 0.373 AC: 56667AN: 151750Hom.: 11089 Cov.: 30 AF XY: 0.374 AC XY: 27716AN XY: 74156
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at