rs60444527

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_006031.6(PCNT):c.6384A>G(p.Thr2128Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0906 in 1,613,756 control chromosomes in the GnomAD database, including 12,077 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.18 ( 4358 hom., cov: 32)

Exomes 𝑓: 0.082 ( 7719 hom. )

Consequence

PCNT
NM_006031.6 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: -0.488

Variant links:

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]

PCNT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 21-46416302-A-G is Benign according to our data. Variant chr21-46416302-A-G is described in ClinVar as [Benign]. Clinvar id is 138623.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-46416302-A-G is described in Lovd as [Likely_benign]. Variant chr21-46416302-A-G is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.488 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCNT	NM_006031.6 link	c.6384A>G	p.Thr2128Thr	synonymous_variant	Exon 30 of 47	ENST00000359568.10	NP_006022.3	O95613-1
PCNT	NM_001315529.2 link	c.6030A>G	p.Thr2010Thr	synonymous_variant	Exon 30 of 47		NP_001302458.1	O95613-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCNT	ENST00000359568.10 link	c.6384A>G	p.Thr2128Thr	synonymous_variant	Exon 30 of 47	1	NM_006031.6	ENSP00000352572.5		O95613-1

Frequencies

GnomAD3 genomes

AF:

0.176

AC:

26807

AN:

151920

Hom.:

4353

Cov.:

show subpopulations

Gnomad AFR

AF:

0.434

Gnomad AMI

AF:

0.0274

Gnomad AMR

AF:

0.0940

Gnomad ASJ

AF:

0.0865

Gnomad EAS

AF:

0.00558

Gnomad SAS

AF:

0.0916

Gnomad FIN

AF:

0.106

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.0762

Gnomad OTH

AF:

0.162

GnomAD3 exomes

AF:

0.0958

AC:

24075

AN:

251426

Hom.:

2216

AF XY:

0.0904

AC XY:

12282

AN XY:

135894

show subpopulations

Gnomad AFR exome

AF:

0.444

Gnomad AMR exome

AF:

0.0551

Gnomad ASJ exome

AF:

0.0863

Gnomad EAS exome

AF:

0.00315

Gnomad SAS exome

AF:

0.0879

Gnomad FIN exome

AF:

0.108

Gnomad NFE exome

AF:

0.0747

Gnomad OTH exome

AF:

0.0823

GnomAD4 exome

AF:

0.0817

AC:

119430

AN:

1461718

Hom.:

7719

Cov.:

AF XY:

0.0808

AC XY:

58786

AN XY:

727172

show subpopulations

Gnomad4 AFR exome

AF:

0.456

Gnomad4 AMR exome

AF:

0.0597

Gnomad4 ASJ exome

AF:

0.0849

Gnomad4 EAS exome

AF:

0.00169

Gnomad4 SAS exome

AF:

0.0849

Gnomad4 FIN exome

AF:

0.103

Gnomad4 NFE exome

AF:

0.0720

Gnomad4 OTH exome

AF:

0.0974

GnomAD4 genome

AF:

0.177

AC:

26845

AN:

152038

Hom.:

4358

Cov.:

AF XY:

0.173

AC XY:

12869

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.433

Gnomad4 AMR

AF:

0.0937

Gnomad4 ASJ

AF:

0.0865

Gnomad4 EAS

AF:

0.00559

Gnomad4 SAS

AF:

0.0914

Gnomad4 FIN

AF:

0.106

Gnomad4 NFE

AF:

0.0762

Gnomad4 OTH

AF:

0.166

Alfa

AF:

0.125

Hom.:

1014

Bravo

AF:

0.187

Asia WGS

AF:

0.103

AC:

357

AN:

3478

EpiCase

AF:

0.0702

EpiControl

AF:

0.0705

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Microcephalic osteodysplastic primordial dwarfism type II

Benign:3

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jun 28, 2017

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not specified

Benign:2

Feb 08, 2013

Genetic Services Laboratory, University of Chicago

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 26, 2014

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.13

DANN

Benign

0.30

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over