chr10-3101411-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002627.5(PFKP):c.311G>A(p.Arg104Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000166 in 1,604,638 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 Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00018 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00017 ( 0 hom. )
Consequence
PFKP
NM_002627.5 missense
NM_002627.5 missense
Scores
1
5
8
Clinical Significance
Conservation
PhyloP100: 5.10
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 Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.22592002).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PFKP | NM_002627.5 | c.311G>A | p.Arg104Gln | missense_variant | 4/22 | ENST00000381125.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PFKP | ENST00000381125.9 | c.311G>A | p.Arg104Gln | missense_variant | 4/22 | 1 | NM_002627.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000177 AC: 27AN: 152190Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000225 AC: 52AN: 230638Hom.: 0 AF XY: 0.000271 AC XY: 34AN XY: 125438
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GnomAD4 exome AF: 0.000165 AC: 240AN: 1452330Hom.: 0 Cov.: 32 AF XY: 0.000168 AC XY: 121AN XY: 721844
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GnomAD4 genome AF: 0.000177 AC: 27AN: 152308Hom.: 0 Cov.: 31 AF XY: 0.000148 AC XY: 11AN XY: 74480
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2022 | The c.311G>A (p.R104Q) alteration is located in exon 4 (coding exon 4) of the PFKP gene. This alteration results from a G to A substitution at nucleotide position 311, causing the arginine (R) at amino acid position 104 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Pathogenic
D;D;D;D
M_CAP
Uncertain
D
MetaRNN
Benign
T;T;T;T
MetaSVM
Uncertain
D
MutationTaster
Benign
D;D
PrimateAI
Benign
T
Sift4G
Benign
T;D;D;T
Polyphen
0.99
.;D;.;.
Vest4
0.51, 0.53
MVP
MPC
0.59
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at