Genetic Variant TATDN2:c.949-42A>G (chr3-10270089-A-G) – 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.949-42A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 1,563,092 control chromosomes in the GnomAD database, including 40,813 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 0.20 ( 4448 hom., cov: 32)

Exomes 𝑓: 0.19 ( 36365 hom. )

Consequence

TATDN2
NM_014760.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.673

Publications

13 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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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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TATDN2	NM_014760.4 link	c.949-42A>G		intron_variant	Intron 3 of 7	ENST00000448281.7	NP_055575.3	Q93075A0A024R2F3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
TATDN2	ENST00000448281.7 link	c.949-42A>G	intron_variant	Intron 3 of 7	1	NM_014760.4	ENSP00000408736.2	Q93075
TATDN2	ENST00000287652.8 link	c.949-42A>G	intron_variant	Intron 3 of 7	1		ENSP00000287652.4	Q93075
ENSG00000272410	ENST00000437082.5 link	n.778-42A>G	intron_variant	Intron 2 of 7	2		ENSP00000402783.1	H7C1W4
ENSG00000272410	ENST00000450534.1 link	n.*393-42A>G	intron_variant	Intron 2 of 7	2		ENSP00000399689.1	H7C1D0

Frequencies

GnomAD3 genomes

AF:

0.205

AC:

31144

AN:

152006

Hom.:

4445

Cov.:

show subpopulations

Gnomad AFR

AF:

0.171

Gnomad AMI

AF:

0.110

Gnomad AMR

AF:

0.354

Gnomad ASJ

AF:

0.124

Gnomad EAS

AF:

0.679

Gnomad SAS

AF:

0.445

Gnomad FIN

AF:

0.210

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.144

Gnomad OTH

AF:

0.189

GnomAD2 exomes

AF:

0.289

AC:

60788

AN:

210360

AF XY:

0.281

show subpopulations

Gnomad AFR exome

AF:

0.172

Gnomad AMR exome

AF:

0.549

Gnomad ASJ exome

AF:

0.122

Gnomad EAS exome

AF:

0.698

Gnomad FIN exome

AF:

0.218

Gnomad NFE exome

AF:

0.149

Gnomad OTH exome

AF:

0.232

GnomAD4 exome

AF:

0.189

AC:

266258

AN:

1410968

Hom.:

36365

Cov.:

AF XY:

0.193

AC XY:

134509

AN XY:

696448

show subpopulations

African (AFR)

AF:

0.167

AC:

5353

AN:

32116

American (AMR)

AF:

0.525

AC:

20544

AN:

39156

Ashkenazi Jewish (ASJ)

AF:

0.116

AC:

2578

AN:

22304

East Asian (EAS)

AF:

0.679

AC:

26740

AN:

39360

South Asian (SAS)

AF:

0.415

AC:

31866

AN:

76824

European-Finnish (FIN)

AF:

0.220

AC:

11225

AN:

50968

Middle Eastern (MID)

AF:

0.179

AC:

763

AN:

4272

European-Non Finnish (NFE)

AF:

0.143

AC:

155583

AN:

1087832

Other (OTH)

AF:

0.200

AC:

11606

AN:

58136

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

10997

21993

32990

43986

54983

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6208

12416

18624

24832

31040

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.205

AC:

31151

AN:

152124

Hom.:

4448

Cov.:

AF XY:

0.217

AC XY:

16137

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.171

AC:

7101

AN:

41516

American (AMR)

AF:

0.355

AC:

5421

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.124

AC:

431

AN:

3470

East Asian (EAS)

AF:

0.679

AC:

3506

AN:

5160

South Asian (SAS)

AF:

0.443

AC:

2135

AN:

4820

European-Finnish (FIN)

AF:

0.210

AC:

2219

AN:

10572

Middle Eastern (MID)

AF:

0.177

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.144

AC:

9782

AN:

67986

Other (OTH)

AF:

0.191

AC:

404

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1172

2344

3517

4689

5861

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

338

676

1014

1352

1690

<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:

0.178

Hom.:

8068

Bravo

AF:

0.217

Asia WGS

AF:

0.509

AC:

1766

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.021

(source)

DANN

Benign

0.51

PhyloP100

-0.67

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over