Genetic Variant DCTD:c.*506G>A (chr4-182890893-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001921.3(DCTD):c.*506G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 152,932 control chromosomes in the GnomAD database, including 10,408 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 0.34 ( 10391 hom., cov: 32)

Exomes 𝑓: 0.18 ( 17 hom. )

Consequence

DCTD
NM_001921.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.79

Publications

10 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCTD	NM_001921.3 link	c.*506G>A		3_prime_UTR_variant	Exon 6 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.*506G>A		3_prime_UTR_variant	Exon 6 of 6	1	NM_001921.3	ENSP00000398194.2		P32321-1

Frequencies

GnomAD3 genomes

AF:

0.339

AC:

51477

AN:

151976

Hom.:

10382

Cov.:

show subpopulations

Gnomad AFR

AF:

0.579

Gnomad AMI

AF:

0.298

Gnomad AMR

AF:

0.322

Gnomad ASJ

AF:

0.199

Gnomad EAS

AF:

0.269

Gnomad SAS

AF:

0.283

Gnomad FIN

AF:

0.211

Gnomad MID

AF:

0.307

Gnomad NFE

AF:

0.234

Gnomad OTH

AF:

0.321

GnomAD4 exome

AF:

0.184

AC:

154

AN:

838

Hom.:

Cov.:

AF XY:

0.191

AC XY:

AN XY:

470

show subpopulations

African (AFR)

AF:

0.625

AC:

AN:

American (AMR)

AF:

0.210

AC:

AN:

138

Ashkenazi Jewish (ASJ)

AF:

0.167

AC:

AN:

East Asian (EAS)

AF:

0.150

AC:

AN:

South Asian (SAS)

AF:

0.180

AC:

AN:

European-Finnish (FIN)

AF:

0.300

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.167

AC:

AN:

580

Other (OTH)

AF:

0.269

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.339

AC:

51518

AN:

152094

Hom.:

10391

Cov.:

AF XY:

0.336

AC XY:

24975

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.579

AC:

23999

AN:

41454

American (AMR)

AF:

0.322

AC:

4929

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.199

AC:

692

AN:

3470

East Asian (EAS)

AF:

0.268

AC:

1385

AN:

5164

South Asian (SAS)

AF:

0.282

AC:

1356

AN:

4812

European-Finnish (FIN)

AF:

0.211

AC:

2234

AN:

10600

Middle Eastern (MID)

AF:

0.299

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.234

AC:

15890

AN:

67990

Other (OTH)

AF:

0.319

AC:

673

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1619

3238

4856

6475

8094

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

482

964

1446

1928

2410

<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.:

4348

Bravo

AF:

0.359

Asia WGS

AF:

0.317

AC:

1100

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.16

(source)

DANN

Benign

0.38

PhyloP100

-1.8

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over