rs17371795

Variant names:

Variant summary

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

The NM_006031.6(PCNT):c.8811A>G(p.Thr2937Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 1,614,024 control chromosomes in the GnomAD database, including 13,937 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1192 hom., cov: 33)

Exomes 𝑓: 0.13 ( 12745 hom. )

Consequence

PCNT
NM_006031.6 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: -2.80

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=-0.93).

BP6

Variant 21-46435963-A-G is Benign according to our data. Variant chr21-46435963-A-G is described in ClinVar as [Benign]. Clinvar id is 95343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-46435963-A-G is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-2.8 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCNT	NM_006031.6 link	c.8811A>G	p.Thr2937Thr	synonymous_variant	Exon 39 of 47	ENST00000359568.10	NP_006022.3	O95613-1
PCNT	NM_001315529.2 link	c.8220A>G	p.Thr2740Thr	synonymous_variant	Exon 39 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.8811A>G	p.Thr2937Thr	synonymous_variant	Exon 39 of 47	1	NM_006031.6	ENSP00000352572.5		O95613-1

Frequencies

GnomAD3 genomes

AF:

0.118

AC:

18024

AN:

152154

Hom.:

1193

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0658

Gnomad AMI

AF:

0.206

Gnomad AMR

AF:

0.157

Gnomad ASJ

AF:

0.124

Gnomad EAS

AF:

0.202

Gnomad SAS

AF:

0.199

Gnomad FIN

AF:

0.158

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.122

Gnomad OTH

AF:

0.114

GnomAD3 exomes

AF:

0.142

AC:

35715

AN:

251106

Hom.:

2820

AF XY:

0.146

AC XY:

19763

AN XY:

135768

show subpopulations

Gnomad AFR exome

AF:

0.0653

Gnomad AMR exome

AF:

0.158

Gnomad ASJ exome

AF:

0.112

Gnomad EAS exome

AF:

0.190

Gnomad SAS exome

AF:

0.209

Gnomad FIN exome

AF:

0.160

Gnomad NFE exome

AF:

0.123

Gnomad OTH exome

AF:

0.129

GnomAD4 exome

AF:

0.127

AC:

185224

AN:

1461752

Hom.:

12745

Cov.:

AF XY:

0.130

AC XY:

94552

AN XY:

727192

show subpopulations

Gnomad4 AFR exome

AF:

0.0662

Gnomad4 AMR exome

AF:

0.160

Gnomad4 ASJ exome

AF:

0.110

Gnomad4 EAS exome

AF:

0.223

Gnomad4 SAS exome

AF:

0.203

Gnomad4 FIN exome

AF:

0.157

Gnomad4 NFE exome

AF:

0.117

Gnomad4 OTH exome

AF:

0.127

GnomAD4 genome

AF:

0.118

AC:

18044

AN:

152272

Hom.:

1192

Cov.:

AF XY:

0.124

AC XY:

9257

AN XY:

74442

show subpopulations

Gnomad4 AFR

AF:

0.0660

Gnomad4 AMR

AF:

0.157

Gnomad4 ASJ

AF:

0.124

Gnomad4 EAS

AF:

0.202

Gnomad4 SAS

AF:

0.199

Gnomad4 FIN

AF:

0.158

Gnomad4 NFE

AF:

0.122

Gnomad4 OTH

AF:

0.115

Alfa

AF:

0.120

Hom.:

1461

Bravo

AF:

0.114

Asia WGS

AF:

0.203

AC:

704

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

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

- -

May 09, 2013

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Microcephalic osteodysplastic primordial dwarfism type II

Benign:1

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. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.40

DANN

Benign

0.37

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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