dbSNP rs3210227: DTWD1:n.-24G>A (chr15-49625144-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000557968.5(DTWD1):n.-24G>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 0.24 in 1,602,110 control chromosomes in the GnomAD database, including 50,386 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 0.19 ( 3510 hom., cov: 32)

Exomes 𝑓: 0.24 ( 46876 hom. )

Consequence

DTWD1
ENST00000557968.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.218

Publications

10 publications found

Variant links:

Genes affected

DTWD1 (HGNC:30926): (DTW domain containing 1) Enables tRNA-uridine aminocarboxypropyltransferase activity. Involved in tRNA modification. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

DTWD1 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=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DTWD1	NM_001144955.2 link	c.-24G>A		5_prime_UTR_variant	Exon 2 of 5	ENST00000403028.8	NP_001138427.1	Q8N5C7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DTWD1	ENST00000403028.8 link	c.-24G>A		5_prime_UTR_variant	Exon 2 of 5	1	NM_001144955.2	ENSP00000385399.3		Q8N5C7-1

Frequencies

GnomAD3 genomes

AF:

0.194

AC:

29420

AN:

151758

Hom.:

3513

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0668

Gnomad AMI

AF:

0.223

Gnomad AMR

AF:

0.180

Gnomad ASJ

AF:

0.260

Gnomad EAS

AF:

0.00483

Gnomad SAS

AF:

0.176

Gnomad FIN

AF:

0.324

Gnomad MID

AF:

0.223

Gnomad NFE

AF:

0.266

Gnomad OTH

AF:

0.210

GnomAD2 exomes

AF:

0.209

AC:

51244

AN:

245284

AF XY:

0.215

show subpopulations

Gnomad AFR exome

AF:

0.0592

Gnomad AMR exome

AF:

0.124

Gnomad ASJ exome

AF:

0.260

Gnomad EAS exome

AF:

0.00120

Gnomad FIN exome

AF:

0.328

Gnomad NFE exome

AF:

0.265

Gnomad OTH exome

AF:

0.249

GnomAD4 exome

AF:

0.245

AC:

354663

AN:

1450234

Hom.:

46876

Cov.:

AF XY:

0.245

AC XY:

176469

AN XY:

721164

show subpopulations

African (AFR)

AF:

0.0585

AC:

1936

AN:

33122

American (AMR)

AF:

0.130

AC:

5728

AN:

44010

Ashkenazi Jewish (ASJ)

AF:

0.263

AC:

6808

AN:

25860

East Asian (EAS)

AF:

0.000936

AC:

AN:

39540

South Asian (SAS)

AF:

0.198

AC:

16877

AN:

85398

European-Finnish (FIN)

AF:

0.324

AC:

17155

AN:

52894

Middle Eastern (MID)

AF:

0.291

AC:

1662

AN:

5718

European-Non Finnish (NFE)

AF:

0.263

AC:

290350

AN:

1103756

Other (OTH)

AF:

0.235

AC:

14110

AN:

59936

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.460

Heterozygous variant carriers

11097

22193

33290

44386

55483

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9414

18828

28242

37656

47070

<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:

0.194

AC:

29410

AN:

151876

Hom.:

3510

Cov.:

AF XY:

0.195

AC XY:

14483

AN XY:

74212

show subpopulations

African (AFR)

AF:

0.0667

AC:

2766

AN:

41440

American (AMR)

AF:

0.179

AC:

2736

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.260

AC:

902

AN:

3470

East Asian (EAS)

AF:

0.00503

AC:

AN:

5168

South Asian (SAS)

AF:

0.175

AC:

840

AN:

4812

European-Finnish (FIN)

AF:

0.324

AC:

3398

AN:

10488

Middle Eastern (MID)

AF:

0.212

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.266

AC:

18039

AN:

67930

Other (OTH)

AF:

0.208

AC:

438

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1166

2332

3499

4665

5831

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

314

628

942

1256

1570

<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:

0.243

Hom.:

2596

Bravo

AF:

0.177

Asia WGS

AF:

0.0770

AC:

267

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

(source)

DANN

Benign

0.86

PhyloP100

0.22

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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