Variant rs3184982 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_152683.4(PRIMPOL):c.1518T>G(p.Gly506Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 1,612,878 control chromosomes in the GnomAD database, including 20,383 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.18 ( 2779 hom., cov: 32)

Exomes 𝑓: 0.15 ( 17604 hom. )

Consequence

PRIMPOL
NM_152683.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.691

Variant links:

Genes affected

PRIMPOL (HGNC:26575): (primase and DNA directed polymerase) This gene encodes a DNA primase-polymerase that belongs to a superfamily of archaeao-eukaryotic primases. Members of this family have primase activity, catalyzing the synthesis of short RNA primers that serve as starting points for DNA synthesis, as well as DNA polymerase activity. The encoded protein facilitates DNA damage tolerance by mediating uninterrupted fork progression after UV irradiation and reinitiating DNA synthesis. An allelic variant in this gene is associated with myopia 22. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]

PRIMPOL links:

CENPU (HGNC:21348): (centromere protein U) The centromere is a specialized chromatin domain, present throughout the cell cycle, that acts as a platform on which the transient assembly of the kinetochore occurs during mitosis. All active centromeres are characterized by the presence of long arrays of nucleosomes in which CENPA (MIM 117139) replaces histone H3 (see MIM 601128). MLF1IP, or CENPU, is an additional factor required for centromere assembly (Foltz et al., 2006 [PubMed 16622419]).[supplied by OMIM, Mar 2008]

CENPU links:

PRIMPOL (HGNC:):

PRIMPOL links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP7

Synonymous conserved (PhyloP=-0.691 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRIMPOL	NM_152683.4 linkuse as main transcript	c.1518T>G	p.Gly506Gly	synonymous_variant	14/14	ENST00000314970.11	NP_689896.1	Q96LW4-1
CENPU	NM_024629.4 linkuse as main transcript	c.*674A>C		3_prime_UTR_variant	13/13	ENST00000281453.10	NP_078905.2	Q71F23-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRIMPOL	ENST00000314970.11 linkuse as main transcript	c.1518T>G	p.Gly506Gly	synonymous_variant	14/14	1	NM_152683.4	ENSP00000313816.6		Q96LW4-1
CENPU	ENST00000281453 linkuse as main transcript	c.*674A>C		3_prime_UTR_variant	13/13	1	NM_024629.4	ENSP00000281453.5		Q71F23-1

Frequencies

GnomAD3 genomes

AF:

0.180

AC:

27390

AN:

151930

Hom.:

2776

Cov.:

show subpopulations

Gnomad AFR

AF:

0.272

Gnomad AMI

AF:

0.208

Gnomad AMR

AF:

0.142

Gnomad ASJ

AF:

0.164

Gnomad EAS

AF:

0.00115

Gnomad SAS

AF:

0.105

Gnomad FIN

AF:

0.146

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.158

Gnomad OTH

AF:

0.191

GnomAD3 exomes

AF:

0.144

AC:

36018

AN:

250094

Hom.:

2971

AF XY:

0.144

AC XY:

19513

AN XY:

135308

show subpopulations

Gnomad AFR exome

AF:

0.274

Gnomad AMR exome

AF:

0.128

Gnomad ASJ exome

AF:

0.170

Gnomad EAS exome

AF:

0.000489

Gnomad SAS exome

AF:

0.118

Gnomad FIN exome

AF:

0.149

Gnomad NFE exome

AF:

0.157

Gnomad OTH exome

AF:

0.148

GnomAD4 exome

AF:

0.151

AC:

219950

AN:

1460830

Hom.:

17604

Cov.:

AF XY:

0.150

AC XY:

108754

AN XY:

726804

show subpopulations

Gnomad4 AFR exome

AF:

0.279

Gnomad4 AMR exome

AF:

0.130

Gnomad4 ASJ exome

AF:

0.168

Gnomad4 EAS exome

AF:

0.000227

Gnomad4 SAS exome

AF:

0.120

Gnomad4 FIN exome

AF:

0.146

Gnomad4 NFE exome

AF:

0.155

Gnomad4 OTH exome

AF:

0.150

GnomAD4 genome

AF:

0.180

AC:

27418

AN:

152048

Hom.:

2779

Cov.:

AF XY:

0.177

AC XY:

13162

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.272

Gnomad4 AMR

AF:

0.142

Gnomad4 ASJ

AF:

0.164

Gnomad4 EAS

AF:

0.00116

Gnomad4 SAS

AF:

0.105

Gnomad4 FIN

AF:

0.146

Gnomad4 NFE

AF:

0.158

Gnomad4 OTH

AF:

0.190

Alfa

AF:

0.168

Hom.:

2786

Bravo

AF:

0.185

Asia WGS

AF:

0.0690

AC:

246

AN:

3478

EpiCase

AF:

0.166

EpiControl

AF:

0.172

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.82

DANN

Benign

0.64

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over