Genetic Variant NM_001921.3:c.*1039G>A (chr4-182890360-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.*1039G>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 0.339 in 152,132 control chromosomes in the GnomAD database, including 10,379 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 ( 10378 hom., cov: 33)

Exomes 𝑓: 0.25 ( 1 hom. )

Consequence

DCTD
NM_001921.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.400

Publications

12 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001921.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
DCTD	NM_001921.3	MANE Select	c.*1039G>A	3_prime_UTR	Exon 6 of 6	NP_001912.2
DCTD	NM_001012732.2		c.*1039G>A	3_prime_UTR	Exon 6 of 6	NP_001012750.1
DCTD	NM_001351743.2		c.*1039G>A	3_prime_UTR	Exon 8 of 8	NP_001338672.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
DCTD	ENST00000438320.7	TSL:1 MANE Select	c.*1039G>A	3_prime_UTR	Exon 6 of 6	ENSP00000398194.2
DCTD	ENST00000357067.7	TSL:1	c.*1039G>A	3_prime_UTR	Exon 6 of 6	ENSP00000349576.3
DCTD	ENST00000500813.6	TSL:2	n.*1314G>A	non_coding_transcript_exon	Exon 5 of 5	ENSP00000425462.1

Frequencies

GnomAD3 genomes

AF:

0.339

AC:

51467

AN:

151982

Hom.:

10367

Cov.:

show subpopulations

Gnomad AFR

AF:

0.579

Gnomad AMI

AF:

0.298

Gnomad AMR

AF:

0.323

Gnomad ASJ

AF:

0.198

Gnomad EAS

AF:

0.269

Gnomad SAS

AF:

0.283

Gnomad FIN

AF:

0.209

Gnomad MID

AF:

0.303

Gnomad NFE

AF:

0.234

Gnomad OTH

AF:

0.321

GnomAD4 exome

AF:

0.250

AC:

AN:

Hom.:

Cov.:

AF XY:

0.292

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.750

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.167

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.533

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

51510

AN:

152100

Hom.:

10378

Cov.:

AF XY:

0.336

AC XY:

24958

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.578

AC:

24005

AN:

41496

American (AMR)

AF:

0.323

AC:

4937

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.198

AC:

688

AN:

3468

East Asian (EAS)

AF:

0.269

AC:

1381

AN:

5142

South Asian (SAS)

AF:

0.282

AC:

1362

AN:

4822

European-Finnish (FIN)

AF:

0.209

AC:

2215

AN:

10582

Middle Eastern (MID)

AF:

0.299

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.234

AC:

15888

AN:

67988

Other (OTH)

AF:

0.319

AC:

674

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1604

3209

4813

6418

8022

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:

0.262

Hom.:

9600

Bravo

AF:

0.359

Asia WGS

AF:

0.317

AC:

1100

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.26

(source)

DANN

Benign

0.59

PhyloP100

-0.40

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