chr10-3103846-C-T
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_002627.5(PFKP):c.522C>T(p.Ile174=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00165 in 1,614,006 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0069 ( 9 hom., cov: 33)
Exomes 𝑓: 0.0011 ( 8 hom. )
Consequence
PFKP
NM_002627.5 synonymous
NM_002627.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.896
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 -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
Variant 10-3103846-C-T is Benign according to our data. Variant chr10-3103846-C-T is described in ClinVar as [Benign]. Clinvar id is 787897.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.896 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0069 (1051/152290) while in subpopulation AFR AF= 0.0224 (931/41574). AF 95% confidence interval is 0.0212. There are 9 homozygotes in gnomad4. There are 495 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 9 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PFKP | NM_002627.5 | c.522C>T | p.Ile174= | synonymous_variant | 5/22 | ENST00000381125.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PFKP | ENST00000381125.9 | c.522C>T | p.Ile174= | synonymous_variant | 5/22 | 1 | NM_002627.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00689 AC: 1048AN: 152172Hom.: 8 Cov.: 33
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GnomAD3 exomes AF: 0.00199 AC: 500AN: 251380Hom.: 5 AF XY: 0.00157 AC XY: 213AN XY: 135898
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GnomAD4 exome AF: 0.00111 AC: 1618AN: 1461716Hom.: 8 Cov.: 33 AF XY: 0.00103 AC XY: 748AN XY: 727170
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GnomAD4 genome AF: 0.00690 AC: 1051AN: 152290Hom.: 9 Cov.: 33 AF XY: 0.00665 AC XY: 495AN XY: 74466
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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 | Aug 16, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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