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GeneBe

rs1052133

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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 0.221 in 152114 control chromosomes in the gnomAD Genomes database, including 4196 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/15 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.22 ( 4196 hom., cov: 32)
Exomes 𝑓: 0.27 ( 11017 hom. )

Consequence

OGG1
NM_002542.6 missense

Scores

16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0730

Links

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (MetaRNN=1.0405932E-4).
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
OGG1NM_002542.6 linkuse as main transcriptc.977C>G p.Ser326Cys missense_variant 7/7 ENST00000344629.12

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
OGG1ENST00000344629.12 linkuse as main transcriptc.977C>G p.Ser326Cys missense_variant 7/71 NM_002542.6 P1O15527-1

Frequencies

GnomAD3 genomes
AF:
0.221
AC:
33640
AN:
152114
Hom.:
4196
Cov.:
32
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
GnomAD3 exomes
AF:
0.274
AC:
68570
AN:
250506
Hom.:
11017
AF XY:
0.270
AC XY:
36667
AN XY:
135562
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 SAS exome
AF:
0.318
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
AF XY:
0.244
AC XY:
177609
AN XY:
727190
show subpopulations
Gnomad4 AFR exome
AF:
0.161
Gnomad4 AMR exome
AF:
0.342
Gnomad4 ASJ exome
AF:
0.208
Gnomad4 EAS exome
AF:
0.531
Gnomad4 SAS exome
AF:
0.317
Gnomad4 FIN exome
AF:
0.184
Gnomad4 NFE exome
AF:
0.228
Gnomad4 OTH exome
AF:
0.251
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

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.083
BayesDel_addAF
Benign
-0.63
T
BayesDel_noAF
Benign
-0.54
Cadd
Benign
5.6
Dann
Benign
0.75
Eigen
Benign
-0.82
Eigen_PC
Benign
-0.92
FATHMM_MKL
Benign
0.096
N
LIST_S2
Benign
0.33
T
MetaRNN
Benign
0.00010
T
MetaSVM
Benign
-0.90
T
MutationTaster
Benign
1.0
P;P;P;P;P;P;P;P
PrimateAI
Benign
0.25
T
PROVEAN
Benign
-0.37
N
REVEL
Benign
0.099
Sift
Benign
0.49
T
Sift4G
Benign
0.17
T
Polyphen
0.10
B
Vest4
0.080
ClinPred
0.0072
T
GERP RS
-1.3
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1052133; hg19: chr3-9798773; COSMIC: COSV56537677; COSMIC: COSV56537677; API