Genetic Variant TATDN2:c.*868C>T (chr3-10280050-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014760.4(TATDN2):c.*868C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 153,742 control chromosomes in the GnomAD database, including 5,687 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 0.26 ( 5669 hom., cov: 32)

Exomes 𝑓: 0.18 ( 18 hom. )

Consequence

TATDN2
NM_014760.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.80

Variant links:

Genes affected

TATDN2 (HGNC:28988): (TatD DNase domain containing 2) Predicted to enable metal ion binding activity and nuclease activity. Predicted to be involved in nucleic acid phosphodiester bond hydrolysis. Predicted to be located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

TATDN2 links:

ENSG00000272410 (HGNC:):

ENSG00000272410 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TATDN2	NM_014760.4 link	c.*868C>T		3_prime_UTR_variant	Exon 8 of 8	ENST00000448281.7	NP_055575.3	Q93075A0A024R2F3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TATDN2	ENST00000448281.7 link	c.*868C>T		3_prime_UTR_variant	Exon 8 of 8	1	NM_014760.4	ENSP00000408736.2		Q93075
ENSG00000272410	ENST00000437082.5 link	n.*223+1016C>T		intron_variant	Intron 7 of 7	2		ENSP00000402783.1		H7C1W4

Frequencies

GnomAD3 genomes

AF:

0.262

AC:

39777

AN:

152020

Hom.:

5651

Cov.:

show subpopulations

Gnomad AFR

AF:

0.359

Gnomad AMI

AF:

0.412

Gnomad AMR

AF:

0.190

Gnomad ASJ

AF:

0.303

Gnomad EAS

AF:

0.0239

Gnomad SAS

AF:

0.216

Gnomad FIN

AF:

0.180

Gnomad MID

AF:

0.266

Gnomad NFE

AF:

0.248

Gnomad OTH

AF:

0.271

GnomAD4 exome

AF:

0.179

AC:

287

AN:

1604

Hom.:

Cov.:

AF XY:

0.174

AC XY:

147

AN XY:

844

show subpopulations

Gnomad4 AFR exome

AF:

0.00

AC:

AN:

Gnomad4 AMR exome

AC:

AN:

Gnomad4 ASJ exome

AC:

AN:

Gnomad4 EAS exome

AF:

0.00

AC:

AN:

Gnomad4 SAS exome

AC:

AN:

Gnomad4 FIN exome

AF:

0.181

AC:

278

AN:

1534

Gnomad4 NFE exome

AF:

0.125

AC:

AN:

Gnomad4 Remaining exome

AF:

0.188

AC:

AN:

Heterozygous variant carriers

109

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.262

AC:

39840

AN:

152138

Hom.:

5669

Cov.:

AF XY:

0.257

AC XY:

19142

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.359

AC:

0.359206

AN:

0.359206

Gnomad4 AMR

AF:

0.190

AC:

0.19

AN:

0.19

Gnomad4 ASJ

AF:

0.303

AC:

0.303345

AN:

0.303345

Gnomad4 EAS

AF:

0.0237

AC:

0.0237269

AN:

0.0237269

Gnomad4 SAS

AF:

0.218

AC:

0.217571

AN:

0.217571

Gnomad4 FIN

AF:

0.180

AC:

0.17986

AN:

0.17986

Gnomad4 NFE

AF:

0.248

AC:

0.248389

AN:

0.248389

Gnomad4 OTH

AF:

0.268

AC:

0.267992

AN:

0.267992

Heterozygous variant carriers

1474

2948

4423

5897

7371

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

408

816

1224

1632

2040

<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:

0.245

Hom.:

11768

Bravo

AF:

0.264

Asia WGS

AF:

0.135

AC:

475

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

4.3

DANN

Benign

0.85

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.2

Mutation Taster

=100/0

polymorphism (auto)

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

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over