rs167715

Positions:

• chr12-103977589-G-A
• chr12-103977589-G-C
• chr12-103977589-G-T

Variant summary

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

The NM_003211.6(TDG):​c.166+529G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.9 in 152,292 control chromosomes in the GnomAD database, including 61,705 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 0.90 (61705 hom., cov: 32)
• Consequence: TDG NM_003211.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TDG	NM_003211.6	c.166+529G>A		intron_variant		ENST00000392872.8	NP_003202.3
TDG	NM_001363612.2	c.-263-2242G>A		intron_variant			NP_001350541.1
TDG	XM_047429486.1	c.154+529G>A		intron_variant			XP_047285442.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TDG	ENST00000392872.8	c.166+529G>A		intron_variant		1	NM_003211.6	ENSP00000376611	P1

Frequencies

GnomAD3 genomes AF: 0.900 AC: 136894 AN: 152174 Hom.: 61665 Cov.: 32

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.921

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.885

Gnomad NFE AF: 0.890

Gnomad OTH AF: 0.896

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

GnomAD4 genome AF: 0.900 AC: 136994 AN: 152292 Hom.: 61705 Cov.: 32 AF XY: 0.903 AC XY: 67254 AN XY: 74474

Gnomad4 AFR AF: 0.883

Gnomad4 AMR AF: 0.921

Gnomad4 ASJ AF: 0.909

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.916

Gnomad4 FIN AF: 0.938

Gnomad4 NFE AF: 0.890

Gnomad4 OTH AF: 0.897

Alfa AF: 0.892 Hom.: 84829

Bravo AF: 0.898

Asia WGS AF: 0.951 AC: 3304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.037
DANN	Benign	0.35

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: rs167715; hg19: chr12-104371367;