dbSNP rs7677967: DCTD:c.*1420T>C (chr4-182889979-A-G) – 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.*1420T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 152,120 control chromosomes in the GnomAD database, including 12,324 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 0.36 ( 12324 hom., cov: 32)

Exomes 𝑓: 0.083 ( 0 hom. )

Consequence

DCTD
NM_001921.3 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.433

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=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCTD	NM_001921.3 link	c.*1420T>C		downstream_gene_variant		ENST00000438320.7	NP_001912.2	P32321-1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
DCTD	ENST00000438320.7 link	c.*1420T>C	downstream_gene_variant	1	NM_001921.3	ENSP00000398194.2	P32321-1
DCTD	ENST00000357067.7 link	c.*1420T>C	downstream_gene_variant	1		ENSP00000349576.3	P32321-2
DCTD	ENST00000500813.6 link	n.*1695T>C	downstream_gene_variant	2		ENSP00000425462.1	D6RD72

Frequencies

GnomAD3 genomes

AF:

0.360

AC:

54741

AN:

151990

Hom.:

12301

Cov.:

show subpopulations

Gnomad AFR

AF:

0.651

Gnomad AMI

AF:

0.298

Gnomad AMR

AF:

0.333

Gnomad ASJ

AF:

0.217

Gnomad EAS

AF:

0.268

Gnomad SAS

AF:

0.284

Gnomad FIN

AF:

0.210

Gnomad MID

AF:

0.323

Gnomad NFE

AF:

0.235

Gnomad OTH

AF:

0.336

GnomAD4 exome

AF:

0.0833

AC:

AN:

Hom.:

AF XY:

0.100

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.250

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.360

AC:

54802

AN:

152108

Hom.:

12324

Cov.:

AF XY:

0.357

AC XY:

26514

AN XY:

74372

show subpopulations

Gnomad4 AFR

AF:

0.650

Gnomad4 AMR

AF:

0.334

Gnomad4 ASJ

AF:

0.217

Gnomad4 EAS

AF:

0.268

Gnomad4 SAS

AF:

0.283

Gnomad4 FIN

AF:

0.210

Gnomad4 NFE

AF:

0.234

Gnomad4 OTH

AF:

0.334

Alfa

AF:

0.306

Hom.:

1098

Bravo

AF:

0.384

Asia WGS

AF:

0.322

AC:

1120

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.40

DANN

Benign

0.41

Splicing

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