chr10-3101452-G-A
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_002627.5(PFKP):c.352G>A(p.Gly118Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000839 in 1,609,982 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00039 ( 2 hom., cov: 31)
Exomes 𝑓: 0.000052 ( 0 hom. )
Consequence
PFKP
NM_002627.5 missense
NM_002627.5 missense
Scores
1
8
5
Clinical Significance
Conservation
PhyloP100: 7.74
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 Likely_benign. Variant got -3 ACMG points.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.752
BS2
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PFKP | NM_002627.5 | c.352G>A | p.Gly118Ser | missense_variant | 4/22 | ENST00000381125.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PFKP | ENST00000381125.9 | c.352G>A | p.Gly118Ser | missense_variant | 4/22 | 1 | NM_002627.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000388 AC: 59AN: 152178Hom.: 2 Cov.: 31
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GnomAD3 exomes AF: 0.000108 AC: 26AN: 241662Hom.: 0 AF XY: 0.0000685 AC XY: 9AN XY: 131306
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GnomAD4 exome AF: 0.0000521 AC: 76AN: 1457804Hom.: 0 Cov.: 32 AF XY: 0.0000441 AC XY: 32AN XY: 724994
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GnomAD4 genome AF: 0.000388 AC: 59AN: 152178Hom.: 2 Cov.: 31 AF XY: 0.000538 AC XY: 40AN XY: 74334
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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 | Apr 07, 2023 | The c.352G>A (p.G118S) 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 352, causing the glycine (G) at amino acid position 118 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D;D
MetaSVM
Uncertain
D
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
Sift4G
Benign
T;D;T;D
Polyphen
0.67
.;P;.;.
Vest4
0.42, 0.43
MutPred
0.79
.;Loss of MoRF binding (P = 0.1385);.;.;
MVP
MPC
0.21
ClinPred
T
GERP RS
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