Genetic Variant DCTD:p.Val105Val (chr4-182894535-A-G) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001921.3(DCTD):c.315T>C(p.Val105Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 1,612,170 control chromosomes in the GnomAD database, including 79,725 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 0.35 ( 9942 hom., cov: 33)

Exomes 𝑓: 0.30 ( 69783 hom. )

Consequence

DCTD
NM_001921.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.264

Publications

31 publications found

Variant links:

Genes affected

DCTD (HGNC:2710): (dCMP deaminase) The protein encoded by this gene catalyzes the deamination of dCMP to dUMP, the nucleotide substrate for thymidylate synthase. The encoded protein is allosterically activated by dCTP and inhibited by dTTP, and is found as a homohexamer. This protein uses zinc as a cofactor for its activity. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

DCTD links:

ENSG00000303565 (HGNC:):

ENSG00000303565 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BP7

Synonymous conserved (PhyloP=0.264 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCTD	NM_001921.3 link	c.315T>C	p.Val105Val	synonymous_variant	Exon 4 of 6	ENST00000438320.7	NP_001912.2	P32321-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCTD	ENST00000438320.7 link	c.315T>C	p.Val105Val	synonymous_variant	Exon 4 of 6	1	NM_001921.3	ENSP00000398194.2		P32321-1

Frequencies

GnomAD3 genomes

AF:

0.347

AC:

52803

AN:

152036

Hom.:

9922

Cov.:

show subpopulations

Gnomad AFR

AF:

0.501

Gnomad AMI

AF:

0.347

Gnomad AMR

AF:

0.220

Gnomad ASJ

AF:

0.224

Gnomad EAS

AF:

0.235

Gnomad SAS

AF:

0.250

Gnomad FIN

AF:

0.340

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.307

Gnomad OTH

AF:

0.293

GnomAD2 exomes

AF:

0.283

AC:

71233

AN:

251298

AF XY:

0.284

show subpopulations

Gnomad AFR exome

AF:

0.504

Gnomad AMR exome

AF:

0.141

Gnomad ASJ exome

AF:

0.237

Gnomad EAS exome

AF:

0.226

Gnomad FIN exome

AF:

0.333

Gnomad NFE exome

AF:

0.309

Gnomad OTH exome

AF:

0.270

GnomAD4 exome

AF:

0.304

AC:

444370

AN:

1460016

Hom.:

69783

Cov.:

AF XY:

0.303

AC XY:

219899

AN XY:

726340

show subpopulations

African (AFR)

AF:

0.504

AC:

16867

AN:

33438

American (AMR)

AF:

0.149

AC:

6643

AN:

44710

Ashkenazi Jewish (ASJ)

AF:

0.235

AC:

6132

AN:

26120

East Asian (EAS)

AF:

0.208

AC:

8247

AN:

39682

South Asian (SAS)

AF:

0.251

AC:

21648

AN:

86212

European-Finnish (FIN)

AF:

0.340

AC:

18137

AN:

53406

Middle Eastern (MID)

AF:

0.267

AC:

1540

AN:

5768

European-Non Finnish (NFE)

AF:

0.312

AC:

346753

AN:

1110350

Other (OTH)

AF:

0.305

AC:

18403

AN:

60330

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.461

Heterozygous variant carriers

14288

28576

42864

57152

71440

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11358

22716

34074

45432

56790

<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:

0.347

AC:

52859

AN:

152154

Hom.:

9942

Cov.:

AF XY:

0.343

AC XY:

25530

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.502

AC:

20818

AN:

41502

American (AMR)

AF:

0.219

AC:

3354

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.224

AC:

778

AN:

3472

East Asian (EAS)

AF:

0.236

AC:

1221

AN:

5184

South Asian (SAS)

AF:

0.250

AC:

1208

AN:

4826

European-Finnish (FIN)

AF:

0.340

AC:

3596

AN:

10584

Middle Eastern (MID)

AF:

0.269

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.307

AC:

20873

AN:

67976

Other (OTH)

AF:

0.291

AC:

616

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1733

3466

5199

6932

8665

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

506

1012

1518

2024

2530

<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:

0.285

Hom.:

5561

Bravo

AF:

0.344

Asia WGS

AF:

0.286

AC:

992

AN:

3478

EpiCase

AF:

0.293

EpiControl

AF:

0.295

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

4.3

(source)

DANN

Benign

0.57

PhyloP100

0.26

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=98/2

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