Genetic Variant TDRD1:c.1384+58C>G (chr10-114206388-C-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_001395205.1(TDRD1):c.1384+58C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 1,407,726 control chromosomes in the GnomAD database, including 36,376 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 0.22 ( 3837 hom., cov: 32)

Exomes 𝑓: 0.22 ( 32539 hom. )

Consequence

TDRD1
NM_001395205.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.25

Publications

5 publications found

Variant links:

Genes affected

TDRD1 (HGNC:11712): (tudor domain containing 1) This gene encodes a protein containing a tudor domain that is thought to function in the suppression of transposable elements during spermatogenesis. The related protein in mouse forms a complex with piRNAs and Piwi proteins to promote methylation and silencing of target sequences. This gene was observed to be upregulated by ETS transcription factor ERG in prostate tumors. [provided by RefSeq, Sep 2018]

TDRD1 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 (NFE) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395205.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TDRD1	NM_001395205.1	MANE Select	c.1384+58C>G	intron	N/A	NP_001382134.1	Q9BXT4-1
TDRD1	NM_001385363.1		c.1384+58C>G	intron	N/A	NP_001372292.1	Q9BXT4-3
TDRD1	NM_198795.2		c.1384+58C>G	intron	N/A	NP_942090.1	Q9BXT4-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TDRD1	ENST00000695399.1	MANE Select	c.1384+58C>G	intron	N/A	ENSP00000511878.1	Q9BXT4-1
TDRD1	ENST00000251864.7	TSL:1	c.1384+58C>G	intron	N/A	ENSP00000251864.2	Q9BXT4-3
TDRD1	ENST00000952550.1		c.1384+58C>G	intron	N/A	ENSP00000622609.1

Frequencies

GnomAD3 genomes

AF:

0.221

AC:

33520

AN:

151934

Hom.:

3833

Cov.:

show subpopulations

Gnomad AFR

AF:

0.220

Gnomad AMI

AF:

0.343

Gnomad AMR

AF:

0.213

Gnomad ASJ

AF:

0.321

Gnomad EAS

AF:

0.0714

Gnomad SAS

AF:

0.125

Gnomad FIN

AF:

0.214

Gnomad MID

AF:

0.275

Gnomad NFE

AF:

0.235

Gnomad OTH

AF:

0.221

GnomAD4 exome

AF:

0.223

AC:

279586

AN:

1255672

Hom.:

32539

AF XY:

0.220

AC XY:

139558

AN XY:

633188

show subpopulations

African (AFR)

AF:

0.221

AC:

6431

AN:

29054

American (AMR)

AF:

0.169

AC:

7150

AN:

42256

Ashkenazi Jewish (ASJ)

AF:

0.321

AC:

7898

AN:

24570

East Asian (EAS)

AF:

0.0771

AC:

2910

AN:

37748

South Asian (SAS)

AF:

0.143

AC:

11339

AN:

79406

European-Finnish (FIN)

AF:

0.216

AC:

10452

AN:

48494

Middle Eastern (MID)

AF:

0.283

AC:

1523

AN:

5388

European-Non Finnish (NFE)

AF:

0.235

AC:

219661

AN:

935098

Other (OTH)

AF:

0.228

AC:

12222

AN:

53658

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

10178

20356

30534

40712

50890

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6978

13956

20934

27912

34890

<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:

0.221

AC:

33566

AN:

152054

Hom.:

3837

Cov.:

AF XY:

0.219

AC XY:

16257

AN XY:

74306

show subpopulations

African (AFR)

AF:

0.220

AC:

9137

AN:

41456

American (AMR)

AF:

0.212

AC:

3241

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.321

AC:

1114

AN:

3470

East Asian (EAS)

AF:

0.0718

AC:

372

AN:

5184

South Asian (SAS)

AF:

0.127

AC:

612

AN:

4824

European-Finnish (FIN)

AF:

0.214

AC:

2257

AN:

10570

Middle Eastern (MID)

AF:

0.272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.235

AC:

15974

AN:

67970

Other (OTH)

AF:

0.222

AC:

468

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1344

2689

4033

5378

6722

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

348

696

1044

1392

1740

<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:

0.123

Hom.:

195

Bravo

AF:

0.222

Asia WGS

AF:

0.125

AC:

437

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.24

(source)

DANN

Benign

0.33

PhyloP100

-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

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over