dbSNP rs5745075: POLE:c.6657+16C>T (chr12-132625629-G-A) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_006231.4(POLE):c.6657+16C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 1,611,794 control chromosomes in the GnomAD database, including 91,794 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.35 ( 10024 hom., cov: 33)

Exomes 𝑓: 0.33 ( 81770 hom. )

Consequence

POLE
NM_006231.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:13

Conservation

PhyloP100: -2.52

Variant links:

Genes affected

POLE (HGNC:9177): (DNA polymerase epsilon, catalytic subunit) This gene encodes the catalytic subunit of DNA polymerase epsilon. The enzyme is involved in DNA repair and chromosomal DNA replication. Mutations in this gene have been associated with colorectal cancer 12 and facial dysmorphism, immunodeficiency, livedo, and short stature. [provided by RefSeq, Sep 2013]

POLE links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 12-132625629-G-A is Benign according to our data. Variant chr12-132625629-G-A is described in ClinVar as [Benign]. Clinvar id is 371835.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-132625629-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
POLE	NM_006231.4 link	c.6657+16C>T	intron_variant	Intron 47 of 48	ENST00000320574.10	NP_006222.2	Q07864
POLE	XM_011534795.4 link	c.6657+16C>T	intron_variant	Intron 47 of 47		XP_011533097.1
POLE	XM_011534797.4 link	c.5736+16C>T	intron_variant	Intron 39 of 39		XP_011533099.1
POLE	XM_011534802.4 link	c.3645+16C>T	intron_variant	Intron 23 of 23		XP_011533104.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POLE	ENST00000320574.10 link	c.6657+16C>T		intron_variant	Intron 47 of 48	1	NM_006231.4	ENSP00000322570.5		Q07864

Frequencies

GnomAD3 genomes

AF:

0.353

AC:

53617

AN:

151992

Hom.:

10011

Cov.:

show subpopulations

Gnomad AFR

AF:

0.366

Gnomad AMI

AF:

0.262

Gnomad AMR

AF:

0.412

Gnomad ASJ

AF:

0.224

Gnomad EAS

AF:

0.693

Gnomad SAS

AF:

0.374

Gnomad FIN

AF:

0.407

Gnomad MID

AF:

0.332

Gnomad NFE

AF:

0.304

Gnomad OTH

AF:

0.342

GnomAD3 exomes

AF:

0.376

AC:

94000

AN:

249782

Hom.:

19475

AF XY:

0.368

AC XY:

49750

AN XY:

135088

show subpopulations

Gnomad AFR exome

AF:

0.365

Gnomad AMR exome

AF:

0.489

Gnomad ASJ exome

AF:

0.233

Gnomad EAS exome

AF:

0.696

Gnomad SAS exome

AF:

0.368

Gnomad FIN exome

AF:

0.401

Gnomad NFE exome

AF:

0.304

Gnomad OTH exome

AF:

0.334

GnomAD4 exome

AF:

0.325

AC:

475107

AN:

1459684

Hom.:

81770

Cov.:

AF XY:

0.327

AC XY:

237143

AN XY:

726222

show subpopulations

Gnomad4 AFR exome

AF:

0.360

Gnomad4 AMR exome

AF:

0.476

Gnomad4 ASJ exome

AF:

0.230

Gnomad4 EAS exome

AF:

0.693

Gnomad4 SAS exome

AF:

0.372

Gnomad4 FIN exome

AF:

0.391

Gnomad4 NFE exome

AF:

0.301

Gnomad4 OTH exome

AF:

0.324

GnomAD4 genome

AF:

0.353

AC:

53646

AN:

152110

Hom.:

10024

Cov.:

AF XY:

0.360

AC XY:

26786

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.365

Gnomad4 AMR

AF:

0.412

Gnomad4 ASJ

AF:

0.224

Gnomad4 EAS

AF:

0.693

Gnomad4 SAS

AF:

0.374

Gnomad4 FIN

AF:

0.407

Gnomad4 NFE

AF:

0.304

Gnomad4 OTH

AF:

0.344

Alfa

AF:

0.314

Hom.:

1438

Bravo

AF:

0.356

Asia WGS

AF:

0.469

AC:

1626

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:13

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:5

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Oct 03, 2016

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Nov 03, 2015

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. -

Clinical Genetics, Academic Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not provided

Benign:4

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 19, 2016

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: The POLE c.6657+16C>T variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a benign outcome for this variant, and 5/5 Alamut algorithms predict no significant change to splicing. This variant was found in 44723/120770 control chromosomes (9098 homozygotes) at a frequency of 0.3703155, which is approximately 26070 times the estimated maximal expected allele frequency of a pathogenic POLE variant (0.0000142), highly suggesting this variant is a benign polymorphism. The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical diagnostic laboratories; nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as Benign. -

Nov 20, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

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

- -

Colorectal cancer, susceptibility to, 12

Benign:2

Jul 07, 2023

KCCC/NGS Laboratory, Kuwait Cancer Control Center

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 14, 2016

Counsyl

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Intrauterine growth retardation, metaphyseal dysplasia, adrenal hypoplasia congenita, genital anomalies, and immunodeficiency

Benign:1

Oct 25, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Facial dysmorphism-immunodeficiency-livedo-short stature syndrome

Benign:1

Oct 25, 2021

Genome-Nilou Lab

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

-0.87

CADD

Benign

0.15

DANN

Benign

0.47

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