chr21-46324123-C-CG
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The 21-46324123-C-CG variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000016 ( 0 hom. )
Consequence
PCNT
NM_006031.6 upstream_gene
NM_006031.6 upstream_gene
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.905
Genes affected
PCNT (HGNC:16068): (pericentrin) The protein encoded by this gene binds to calmodulin and is expressed in the centrosome. It is an integral component of the pericentriolar material (PCM). The protein contains a series of coiled-coil domains and a highly conserved PCM targeting motif called the PACT domain near its C-terminus. The protein interacts with the microtubule nucleation component gamma-tubulin and is likely important to normal functioning of the centrosomes, cytoskeleton, and cell-cycle progression. Mutations in this gene cause Seckel syndrome-4 and microcephalic osteodysplastic primordial dwarfism type II. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCNT | NM_006031.6 | upstream_gene_variant | ENST00000359568.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCNT | ENST00000359568.10 | upstream_gene_variant | 1 | NM_006031.6 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 151928Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.0000159 AC: 12AN: 755790Hom.: 0 Cov.: 0 AF XY: 0.0000177 AC XY: 7AN XY: 394650
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GnomAD4 genome AF: 0.0000263 AC: 4AN: 152044Hom.: 0 Cov.: 0 AF XY: 0.0000269 AC XY: 2AN XY: 74306
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Microcephalic osteodysplastic primordial dwarfism Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at