Genetic Variant DDIT4:n.1087T>A (chr10-72275283-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000473155.2(DDIT4):n.1087T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 1,395,196 control chromosomes in the GnomAD database, including 106,227 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 0.37 ( 11752 hom., cov: 32)

Exomes 𝑓: 0.38 ( 94475 hom. )

Consequence

DDIT4
ENST00000473155.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.91

Publications

27 publications found

Variant links:

Genes affected

DDIT4 (HGNC:24944): (DNA damage inducible transcript 4) Predicted to enable 14-3-3 protein binding activity. Involved in defense response to virus; negative regulation of TOR signaling; and response to hypoxia. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

DDIT4 links:

DDIT4-AS1 (HGNC:):

DDIT4-AS1 links:

Genome browser will be placed here

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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DDIT4	NM_019058.4 link	c.*95T>A		3_prime_UTR_variant	Exon 3 of 3	ENST00000307365.4	NP_061931.1	Q9NX09A0A024QZQ6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DDIT4	ENST00000307365.4 link	c.*95T>A		3_prime_UTR_variant	Exon 3 of 3	1	NM_019058.4	ENSP00000307305.3		Q9NX09

Frequencies

GnomAD3 genomes

AF:

0.374

AC:

56809

AN:

151936

Hom.:

11730

Cov.:

show subpopulations

Gnomad AFR

AF:

0.245

Gnomad AMI

AF:

0.363

Gnomad AMR

AF:

0.456

Gnomad ASJ

AF:

0.378

Gnomad EAS

AF:

0.799

Gnomad SAS

AF:

0.456

Gnomad FIN

AF:

0.551

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.369

Gnomad OTH

AF:

0.354

GnomAD4 exome

AF:

0.379

AC:

471182

AN:

1243142

Hom.:

94475

Cov.:

AF XY:

0.379

AC XY:

232069

AN XY:

612138

show subpopulations

African (AFR)

AF:

0.239

AC:

6794

AN:

28368

American (AMR)

AF:

0.513

AC:

13271

AN:

25882

Ashkenazi Jewish (ASJ)

AF:

0.357

AC:

6829

AN:

19126

East Asian (EAS)

AF:

0.772

AC:

29355

AN:

38002

South Asian (SAS)

AF:

0.422

AC:

27831

AN:

65986

European-Finnish (FIN)

AF:

0.518

AC:

17351

AN:

33514

Middle Eastern (MID)

AF:

0.251

AC:

1206

AN:

4812

European-Non Finnish (NFE)

AF:

0.357

AC:

348358

AN:

974856

Other (OTH)

AF:

0.384

AC:

20187

AN:

52596

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

14328

28656

42984

57312

71640

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11340

22680

34020

45360

56700

<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:

0.374

AC:

56863

AN:

152054

Hom.:

11752

Cov.:

AF XY:

0.388

AC XY:

28840

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.246

AC:

10187

AN:

41474

American (AMR)

AF:

0.457

AC:

6980

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.378

AC:

1313

AN:

3472

East Asian (EAS)

AF:

0.800

AC:

4141

AN:

5176

South Asian (SAS)

AF:

0.454

AC:

2187

AN:

4816

European-Finnish (FIN)

AF:

0.551

AC:

5824

AN:

10562

Middle Eastern (MID)

AF:

0.282

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.369

AC:

25063

AN:

67964

Other (OTH)

AF:

0.358

AC:

755

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1749

3497

5246

6994

8743

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

556

1112

1668

2224

2780

<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:

0.371

Hom.:

1460

Bravo

AF:

0.362

Asia WGS

AF:

0.611

AC:

2128

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

(source)

DANN

Benign

0.59

PhyloP100

1.9

RBP_binding_hub_radar

1.0

RBP_regulation_power_radar

2.2

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over