10-3103786-C-T
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_002627.5(PFKP):c.462C>T(p.Ile154=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.001 in 1,613,876 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00060 ( 1 hom., cov: 33)
Exomes 𝑓: 0.0010 ( 17 hom. )
Consequence
PFKP
NM_002627.5 synonymous
NM_002627.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.151
Genes affected
PFKP (HGNC:8878): (phosphofructokinase, platelet) This gene encodes a member of the phosphofructokinase A protein family. The encoded enzyme is the platelet-specific isoform of phosphofructokinase and plays a key role in glycolysis regulation. This gene may play a role in metabolic reprogramming in some cancers, including clear cell renal cell carcinomas, and cancer of the bladder, breast, and lung. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
Variant 10-3103786-C-T is Benign according to our data. Variant chr10-3103786-C-T is described in ClinVar as [Benign]. Clinvar id is 772942.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.151 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 17 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PFKP | NM_002627.5 | c.462C>T | p.Ile154= | synonymous_variant | 5/22 | ENST00000381125.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PFKP | ENST00000381125.9 | c.462C>T | p.Ile154= | synonymous_variant | 5/22 | 1 | NM_002627.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000578 AC: 88AN: 152224Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00142 AC: 356AN: 250812Hom.: 4 AF XY: 0.00172 AC XY: 233AN XY: 135638
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GnomAD4 exome AF: 0.00104 AC: 1523AN: 1461534Hom.: 17 Cov.: 33 AF XY: 0.00126 AC XY: 917AN XY: 727074
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GnomAD4 genome AF: 0.000597 AC: 91AN: 152342Hom.: 1 Cov.: 33 AF XY: 0.000725 AC XY: 54AN XY: 74496
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 18, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
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