4-127881143-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 2P and 15B. PM2BP4_ModerateBP6_Very_StrongBP7BS1
The NM_014264.5(PLK4):c.9C>T(p.Thr3=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000694 in 1,614,006 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 Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. T3T) has been classified as Likely benign.
Frequency
Consequence
NM_014264.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLK4 | NM_014264.5 | c.9C>T | p.Thr3= | synonymous_variant | 1/16 | ENST00000270861.10 | |
PLK4 | NM_001190799.2 | c.9C>T | p.Thr3= | synonymous_variant | 1/15 | ||
PLK4 | XM_005262701.4 | c.9C>T | p.Thr3= | synonymous_variant | 1/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLK4 | ENST00000270861.10 | c.9C>T | p.Thr3= | synonymous_variant | 1/16 | 1 | NM_014264.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000401 AC: 61AN: 152186Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000839 AC: 21AN: 250254Hom.: 0 AF XY: 0.0000665 AC XY: 9AN XY: 135384
GnomAD4 exome AF: 0.0000349 AC: 51AN: 1461702Hom.: 0 Cov.: 31 AF XY: 0.0000303 AC XY: 22AN XY: 727144
GnomAD4 genome ? AF: 0.000401 AC: 61AN: 152304Hom.: 0 Cov.: 33 AF XY: 0.000430 AC XY: 32AN XY: 74484
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 04, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2024 | PLK4: BP4, BP7 - |
PLK4-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 08, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at