chr12-103978878-A-G

Position:

• chr12-103978878-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003211.6(TDG):​c.167-953A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 151,760 control chromosomes in the GnomAD database, including 27,975 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.60 (27975 hom., cov: 29)
• Consequence: TDG NM_003211.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.991

Genes affected

TDG (HGNC:11700): (thymine DNA glycosylase) The protein encoded by this gene belongs to the TDG/mug DNA glycosylase family. Thymine-DNA glycosylase (TDG) removes thymine moieties from G/T mismatches by hydrolyzing the carbon-nitrogen bond between the sugar-phosphate backbone of DNA and the mispaired thymine. With lower activity, this enzyme also removes thymine from C/T and T/T mispairings. TDG can also remove uracil and 5-bromouracil from mispairings with guanine. This enzyme plays a central role in cellular defense against genetic mutation caused by the spontaneous deamination of 5-methylcytosine and cytosine. This gene may have a pseudogene in the p arm of chromosome 12. [provided by RefSeq, Jul 2008]

TDG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TDG	NM_003211.6	c.167-953A>G		intron_variant		ENST00000392872.8	NP_003202.3
TDG	NM_001363612.2	c.-263-953A>G		intron_variant			NP_001350541.1
TDG	XM_047429486.1	c.155-953A>G		intron_variant			XP_047285442.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TDG	ENST00000392872.8	c.167-953A>G		intron_variant		1	NM_003211.6	ENSP00000376611.3

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91624 AN: 151640 Hom.: 27961 Cov.: 29

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.589

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.604 AC: 91684 AN: 151760 Hom.: 27975 Cov.: 29 AF XY: 0.610 AC XY: 45206 AN XY: 74158

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.535

Gnomad4 SAS AF: 0.727

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.590

Alfa AF: 0.608 Hom.: 36140

Bravo AF: 0.586

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.7
DANN	Benign	0.62

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

Other links and lift over

dbSNP: rs10861152; hg19: chr12-104372656;