Variant 4-182890893-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
DCTD	NM_001921.3 link	c.*506G>A		3_prime_UTR_variant	6/6	ENST00000438320.7	NP_001912.2	P32321-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DCTD	ENST00000438320 link	c.*506G>A		3_prime_UTR_variant	6/6	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

Gnomad4 AFR exome

AF:

0.625

Gnomad4 AMR exome

AF:

0.210

Gnomad4 ASJ exome

AF:

0.167

Gnomad4 EAS exome

AF:

0.150

Gnomad4 SAS exome

AF:

0.180

Gnomad4 FIN exome

AF:

0.300

Gnomad4 NFE exome

AF:

0.167

Gnomad4 OTH exome

AF:

0.269

GnomAD4 genome

AF:

0.339

AC:

51518

AN:

152094

Hom.:

10391

Cov.:

AF XY:

0.336

AC XY:

24975

AN XY:

74364

show subpopulations

Gnomad4 AFR

AF:

0.579

Gnomad4 AMR

AF:

0.322

Gnomad4 ASJ

AF:

0.199

Gnomad4 EAS

AF:

0.268

Gnomad4 SAS

AF:

0.282

Gnomad4 FIN

AF:

0.211

Gnomad4 NFE

AF:

0.234

Gnomad4 OTH

AF:

0.319

Alfa

AF:

0.283

Hom.:

2709

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

DANN

Benign

0.38

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.2

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over