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

Publications

15 publications found

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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new If you want to explore the variant's impact on the transcript NM_014760.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014760.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TATDN2	NM_014760.4	MANE Select	c.*868C>T		3_prime_UTR	Exon 8 of 8	NP_055575.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TATDN2	ENST00000448281.7	TSL:1 MANE Select	c.*868C>T	3_prime_UTR	Exon 8 of 8	ENSP00000408736.2	Q93075
TATDN2	ENST00000287652.8	TSL:1	c.*839C>T	3_prime_UTR	Exon 8 of 8	ENSP00000287652.4	Q93075
ENSG00000272410	ENST00000437082.5	TSL:2	n.*223+1016C>T	intron	N/A	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

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.181

AC:

278

AN:

1534

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.125

AC:

AN:

Other (OTH)

AF:

0.188

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

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

African (AFR)

AF:

0.359

AC:

14897

AN:

41472

American (AMR)

AF:

0.190

AC:

2907

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.303

AC:

1052

AN:

3468

East Asian (EAS)

AF:

0.0237

AC:

123

AN:

5184

South Asian (SAS)

AF:

0.218

AC:

1050

AN:

4826

European-Finnish (FIN)

AF:

0.180

AC:

1904

AN:

10586

Middle Eastern (MID)

AF:

0.269

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.248

AC:

16888

AN:

67990

Other (OTH)

AF:

0.268

AC:

566

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1474

2948

4423

5897

7371

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

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 v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

4.3

(source)

DANN

Benign

0.85

PhyloP100

-1.8

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.2

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over