chr3-9751913-A-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_002542.6(OGG1):​c.529A>C​(p.Thr177Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

OGG1
NM_002542.6 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.134
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.109392285).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
OGG1NM_002542.6 linkc.529A>C p.Thr177Pro missense_variant Exon 3 of 7 ENST00000344629.12 NP_002533.1 O15527-1E5KPN1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
OGG1ENST00000344629.12 linkc.529A>C p.Thr177Pro missense_variant Exon 3 of 7 1 NM_002542.6 ENSP00000342851.7 O15527-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.087
BayesDel_addAF
Benign
-0.11
T
BayesDel_noAF
Benign
-0.39
CADD
Benign
16
DANN
Benign
0.94
DEOGEN2
Benign
0.077
.;T;.;.;.;.;.;.
Eigen
Benign
-0.90
Eigen_PC
Benign
-0.83
FATHMM_MKL
Benign
0.052
N
LIST_S2
Benign
0.67
T;T;T;T;T;T;T;T
M_CAP
Benign
0.0077
T
MetaRNN
Benign
0.11
T;T;T;T;T;T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
-0.025
N;N;N;N;N;N;N;N
PrimateAI
Benign
0.43
T
PROVEAN
Benign
-0.66
N;N;N;N;N;N;N;N
REVEL
Benign
0.13
Sift
Benign
0.41
T;T;T;T;T;T;T;T
Sift4G
Benign
0.54
T;T;T;T;T;T;T;T
Polyphen
0.0
.;B;.;.;B;.;.;.
Vest4
0.23
MutPred
0.49
Gain of glycosylation at Y178 (P = 0.0079);Gain of glycosylation at Y178 (P = 0.0079);Gain of glycosylation at Y178 (P = 0.0079);Gain of glycosylation at Y178 (P = 0.0079);Gain of glycosylation at Y178 (P = 0.0079);Gain of glycosylation at Y178 (P = 0.0079);Gain of glycosylation at Y178 (P = 0.0079);Gain of glycosylation at Y178 (P = 0.0079);
MVP
0.47
MPC
0.13
ClinPred
0.16
T
GERP RS
-3.5
Varity_R
0.23
gMVP
0.68

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs144249605; hg19: chr3-9793597; API