rs6941583

Positions:

chr6-43614354-A-T

Variant summary

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

The NM_006502.3(POLH):c.1939A>T(p.Met647Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0491 in 1,612,354 control chromosomes in the GnomAD database, including 5,137 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M647R) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.11 ( 2157 hom., cov: 32)

Exomes 𝑓: 0.042 ( 2980 hom. )

Consequence

POLH
NM_006502.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 2.90

Variant links:

Genes affected

POLH (HGNC:9181): (DNA polymerase eta) This gene encodes a member of the Y family of specialized DNA polymerases. It copies undamaged DNA with a lower fidelity than other DNA-directed polymerases. However, it accurately replicates UV-damaged DNA; when thymine dimers are present, this polymerase inserts the complementary nucleotides in the newly synthesized DNA, thereby bypassing the lesion and suppressing the mutagenic effect of UV-induced DNA damage. This polymerase is thought to be involved in hypermutation during immunoglobulin class switch recombination. Mutations in this gene result in XPV, a variant type of xeroderma pigmentosum. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2014]

POLH links:

POLR1C (HGNC:):

POLR1C links:

GTPBP2 (HGNC:4670): (GTP binding protein 2) GTP-binding proteins, or G proteins, constitute a superfamily capable of binding GTP or GDP. G proteins are activated by binding GTP and are inactivated by hydrolyzing GTP to GDP. This general mechanism enables G proteins to perform a wide range of biologic activities.[supplied by OMIM, Jan 2003]

GTPBP2 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 (MetaRNN=0.0013748407).

BP6

Variant 6-43614354-A-T is Benign according to our data. Variant chr6-43614354-A-T is described in ClinVar as [Benign]. Clinvar id is 259989.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POLH	NM_006502.3 linkuse as main transcript	c.1939A>T	p.Met647Leu	missense_variant	11/11	ENST00000372236.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POLH	ENST00000372236.9 linkuse as main transcript	c.1939A>T	p.Met647Leu	missense_variant	11/11	1	NM_006502.3	P1	Q9Y253-1
POLH	ENST00000372226.1 linkuse as main transcript	c.*623A>T		3_prime_UTR_variant	11/11	1			Q9Y253-2
GTPBP2	ENST00000496137.5 linkuse as main transcript	c.*131+5765T>A		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.113

AC:

17193

AN:

152102

Hom.:

2139

Cov.:

show subpopulations

Gnomad AFR

AF:

0.310

Gnomad AMI

AF:

0.0164

Gnomad AMR

AF:

0.0570

Gnomad ASJ

AF:

0.0490

Gnomad EAS

AF:

0.0366

Gnomad SAS

AF:

0.0826

Gnomad FIN

AF:

0.0380

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0310

Gnomad OTH

AF:

0.0899

GnomAD3 exomes

AF:

0.0591

AC:

14840

AN:

251254

Hom.:

1123

AF XY:

0.0560

AC XY:

7598

AN XY:

135790

show subpopulations

Gnomad AFR exome

AF:

0.321

Gnomad AMR exome

AF:

0.0284

Gnomad ASJ exome

AF:

0.0538

Gnomad EAS exome

AF:

0.0391

Gnomad SAS exome

AF:

0.0855

Gnomad FIN exome

AF:

0.0388

Gnomad NFE exome

AF:

0.0318

Gnomad OTH exome

AF:

0.0509

GnomAD4 exome

AF:

0.0424

AC:

61839

AN:

1460134

Hom.:

2980

Cov.:

AF XY:

0.0428

AC XY:

31042

AN XY:

726010

show subpopulations

Gnomad4 AFR exome

AF:

0.321

Gnomad4 AMR exome

AF:

0.0327

Gnomad4 ASJ exome

AF:

0.0552

Gnomad4 EAS exome

AF:

0.0340

Gnomad4 SAS exome

AF:

0.0800

Gnomad4 FIN exome

AF:

0.0365

Gnomad4 NFE exome

AF:

0.0309

Gnomad4 OTH exome

AF:

0.0547

GnomAD4 genome

AF:

0.113

AC:

17262

AN:

152220

Hom.:

2157

Cov.:

AF XY:

0.112

AC XY:

8316

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.311

Gnomad4 AMR

AF:

0.0570

Gnomad4 ASJ

AF:

0.0490

Gnomad4 EAS

AF:

0.0367

Gnomad4 SAS

AF:

0.0825

Gnomad4 FIN

AF:

0.0380

Gnomad4 NFE

AF:

0.0310

Gnomad4 OTH

AF:

0.0899

Alfa

AF:

0.0463

Hom.:

287

Bravo

AF:

0.123

TwinsUK

AF:

0.0283

AC:

105

ALSPAC

AF:

0.0304

AC:

117

ESP6500AA

AF:

0.305

AC:

1343

ESP6500EA

AF:

0.0308

AC:

265

ExAC

AF:

0.0654

AC:

7941

Asia WGS

AF:

0.0850

AC:

297

AN:

3478

EpiCase

AF:

0.0337

EpiControl

AF:

0.0344

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Xeroderma pigmentosum variant type

Benign:2

Benign, criteria provided, single submitter	clinical testing	KCCC/NGS Laboratory, Kuwait Cancer Control Center	Jul 07, 2023	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 12, 2018	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 provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 09, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Feb 01, 2024	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.48

BayesDel_noAF

Benign

-0.32

CADD

Benign

DANN

Benign

0.84

DEOGEN2

Benign

0.070

Eigen

Benign

-0.12

Eigen_PC

Benign

0.070

FATHMM_MKL

Uncertain

0.87

LIST_S2

Benign

0.61

MetaRNN

Benign

0.0014

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.3

MutationTaster

Benign

0.15

P;P

PrimateAI

Benign

0.42

PROVEAN

Benign

-0.23

REVEL

Benign

0.14

Sift

Benign

0.51

Sift4G

Benign

0.61

Polyphen

0.030

Vest4

0.11

MutPred

0.19

Loss of catalytic residue at M647 (P = 0.1213);

MPC

0.20

ClinPred

0.016

GERP RS

5.7

Varity_R

0.41

gMVP

0.47

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