rs2838549
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002626.6(PFKL):c.747+981G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0844 in 152,318 control chromosomes in the GnomAD database, including 578 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 0.084 ( 578 hom., cov: 34)
Exomes 𝑓: 0.038 ( 0 hom. )
Consequence
PFKL
NM_002626.6 intron
NM_002626.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -6.30
Genes affected
PFKL (HGNC:8876): (phosphofructokinase, liver type) This gene encodes the liver (L) subunit of an enzyme that catalyzes the conversion of D-fructose 6-phosphate to D-fructose 1,6-bisphosphate, which is a key step in glucose metabolism (glycolysis). This enzyme is a tetramer that may be composed of different subunits encoded by distinct genes in different tissues. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]
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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=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PFKL | NM_002626.6 | c.747+981G>A | intron_variant | ENST00000349048.9 | NP_002617.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PFKL | ENST00000349048.9 | c.747+981G>A | intron_variant | 1 | NM_002626.6 | ENSP00000269848.6 | ||||
PFKL | ENST00000397961.6 | n.*1096+981G>A | intron_variant | 1 | ENSP00000381052.2 | |||||
PFKL | ENST00000466134.5 | n.1738G>A | non_coding_transcript_exon_variant | 7/20 | 2 | |||||
PFKL | ENST00000496824.5 | n.967+981G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0845 AC: 12850AN: 152148Hom.: 576 Cov.: 34
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GnomAD4 exome AF: 0.0385 AC: 2AN: 52Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 32
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GnomAD4 genome AF: 0.0845 AC: 12860AN: 152266Hom.: 578 Cov.: 34 AF XY: 0.0839 AC XY: 6244AN XY: 74450
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ClinVar
Not reported inComputational scores
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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