Genetic Variant DCTD:c.108+124G>A (chr4-182915337-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001921.3(DCTD):c.108+124G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 766,396 control chromosomes in the GnomAD database, including 15,728 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 0.17 ( 2359 hom., cov: 33)

Exomes 𝑓: 0.20 ( 13369 hom. )

Consequence

DCTD
NM_001921.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.826

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=-0.8).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCTD	NM_001921.3 link	c.108+124G>A		intron_variant	Intron 2 of 5	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.108+124G>A		intron_variant	Intron 2 of 5	1	NM_001921.3	ENSP00000398194.2		P32321-1

Frequencies

GnomAD3 genomes

AF:

0.168

AC:

25489

AN:

152094

Hom.:

2360

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0832

Gnomad AMI

AF:

0.179

Gnomad AMR

AF:

0.136

Gnomad ASJ

AF:

0.141

Gnomad EAS

AF:

0.261

Gnomad SAS

AF:

0.175

Gnomad FIN

AF:

0.182

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.218

Gnomad OTH

AF:

0.156

GnomAD4 exome

AF:

0.205

AC:

125807

AN:

614184

Hom.:

13369

AF XY:

0.204

AC XY:

66597

AN XY:

325970

show subpopulations

Gnomad4 AFR exome

AF:

0.0860

Gnomad4 AMR exome

AF:

0.138

Gnomad4 ASJ exome

AF:

0.153

Gnomad4 EAS exome

AF:

0.232

Gnomad4 SAS exome

AF:

0.174

Gnomad4 FIN exome

AF:

0.199

Gnomad4 NFE exome

AF:

0.221

Gnomad4 OTH exome

AF:

0.195

GnomAD4 genome

AF:

0.167

AC:

25484

AN:

152212

Hom.:

2359

Cov.:

AF XY:

0.167

AC XY:

12407

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.0830

Gnomad4 AMR

AF:

0.136

Gnomad4 ASJ

AF:

0.141

Gnomad4 EAS

AF:

0.261

Gnomad4 SAS

AF:

0.175

Gnomad4 FIN

AF:

0.182

Gnomad4 NFE

AF:

0.218

Gnomad4 OTH

AF:

0.156

Alfa

AF:

0.201

Hom.:

2296

Bravo

AF:

0.162

Asia WGS

AF:

0.220

AC:

764

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.27

DANN

Benign

0.79

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