Genetic Variant OGG1:p.Ser326Cys (chr3-9757089-C-G) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_002542.6(OGG1):c.977C>G(p.Ser326Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 1,614,026 control chromosomes in the GnomAD database, including 50,216 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.22 ( 4185 hom., cov: 32)

Exomes 𝑓: 0.24 ( 46031 hom. )

Consequence

OGG1
NM_002542.6 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.0730

Publications

783 publications found

Variant links:

Genes affected

OGG1 (HGNC:8125): (8-oxoguanine DNA glycosylase) This gene encodes the enzyme responsible for the excision of 8-oxoguanine, a mutagenic base byproduct which occurs as a result of exposure to reactive oxygen. The action of this enzyme includes lyase activity for chain cleavage. Alternative splicing of the C-terminal region of this gene classifies splice variants into two major groups, type 1 and type 2, depending on the last exon of the sequence. Type 1 alternative splice variants end with exon 7 and type 2 end with exon 8. All variants share the N-terminal region in common, which contains a mitochondrial targeting signal that is essential for mitochondrial localization. Many alternative splice variants for this gene have been described, but the full-length nature for every variant has not been determined. [provided by RefSeq, Aug 2008]

OGG1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.0405932E-4).

BP6

Variant 3-9757089-C-G is Benign according to our data. Variant chr3-9757089-C-G is described in ClinVar as Benign. ClinVar VariationId is 3059470.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OGG1	NM_002542.6 link	c.977C>G	p.Ser326Cys	missense_variant	Exon 7 of 7	ENST00000344629.12	NP_002533.1	O15527-1E5KPN1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OGG1	ENST00000344629.12 link	c.977C>G	p.Ser326Cys	missense_variant	Exon 7 of 7	1	NM_002542.6	ENSP00000342851.7		O15527-1

Frequencies

GnomAD3 genomes

AF:

0.221

AC:

33640

AN:

152114

Hom.:

4196

Cov.:

show subpopulations

Gnomad AFR

AF:

0.165

Gnomad AMI

AF:

0.173

Gnomad AMR

AF:

0.244

Gnomad ASJ

AF:

0.197

Gnomad EAS

AF:

0.572

Gnomad SAS

AF:

0.331

Gnomad FIN

AF:

0.193

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.222

Gnomad OTH

AF:

0.227

GnomAD2 exomes

AF:

0.274

AC:

68570

AN:

250506

AF XY:

0.270

show subpopulations

Gnomad AFR exome

AF:

0.164

Gnomad AMR exome

AF:

0.358

Gnomad ASJ exome

AF:

0.215

Gnomad EAS exome

AF:

0.596

Gnomad FIN exome

AF:

0.184

Gnomad NFE exome

AF:

0.223

Gnomad OTH exome

AF:

0.250

GnomAD4 exome

AF:

0.243

AC:

355035

AN:

1461794

Hom.:

46031

Cov.:

AF XY:

0.244

AC XY:

177609

AN XY:

727190

show subpopulations

African (AFR)

AF:

0.161

AC:

5386

AN:

33478

American (AMR)

AF:

0.342

AC:

15289

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.208

AC:

5425

AN:

26136

East Asian (EAS)

AF:

0.531

AC:

21093

AN:

39698

South Asian (SAS)

AF:

0.317

AC:

27331

AN:

86256

European-Finnish (FIN)

AF:

0.184

AC:

9841

AN:

53340

Middle Eastern (MID)

AF:

0.315

AC:

1819

AN:

5768

European-Non Finnish (NFE)

AF:

0.228

AC:

253669

AN:

1112000

Other (OTH)

AF:

0.251

AC:

15182

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

17819

35638

53456

71275

89094

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9046

18092

27138

36184

45230

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.221

AC:

33628

AN:

152232

Hom.:

4185

Cov.:

AF XY:

0.220

AC XY:

16365

AN XY:

74410

show subpopulations

African (AFR)

AF:

0.164

AC:

6828

AN:

41534

American (AMR)

AF:

0.244

AC:

3730

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.197

AC:

685

AN:

3470

East Asian (EAS)

AF:

0.572

AC:

2959

AN:

5176

South Asian (SAS)

AF:

0.330

AC:

1590

AN:

4824

European-Finnish (FIN)

AF:

0.193

AC:

2039

AN:

10586

Middle Eastern (MID)

AF:

0.330

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.222

AC:

15069

AN:

68020

Other (OTH)

AF:

0.224

AC:

473

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1368

2736

4103

5471

6839

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

372

744

1116

1488

1860

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.221

Hom.:

1284

Bravo

AF:

0.228

TwinsUK

AF:

0.232

AC:

859

ALSPAC

AF:

0.225

AC:

868

ESP6500AA

AF:

0.174

AC:

767

ESP6500EA

AF:

0.230

AC:

1979

ExAC

AF:

0.271

AC:

32872

Asia WGS

AF:

0.386

AC:

1340

AN:

3478

EpiCase

AF:

0.230

EpiControl

AF:

0.229

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

OGG1-related disorder

Benign:1

Oct 17, 2019

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.083

BayesDel_addAF

Benign

-0.63

BayesDel_noAF

Benign

-0.54

CADD

Benign

8.3

(source)

DANN

Benign

0.75

Eigen

Benign

-0.82

Eigen_PC

Benign

-0.92

FATHMM_MKL

Benign

0.096

LIST_S2

Benign

0.33

MetaRNN

Benign

0.00010

MetaSVM

Benign

-0.90

PhyloP100

-0.073

PrimateAI

Benign

0.25

PROVEAN

Benign

-0.37

REVEL

Benign

0.099

Sift

Benign

0.49

Sift4G

Benign

0.17

Polyphen

0.10

Vest4

0.080

ClinPred

0.0072

GERP RS

-1.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.037

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over