rs13137332

Positions:

• chr4-182903883-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001921.3(DCTD):​c.245-9278A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0485 in 152,168 control chromosomes in the GnomAD database, including 264 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 0.049 (264 hom., cov: 32)
• Consequence: DCTD NM_001921.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCTD	NM_001921.3	c.245-9278A>G		intron_variant		ENST00000438320.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCTD	ENST00000438320.7	c.245-9278A>G		intron_variant		1	NM_001921.3	P1

Frequencies

GnomAD3 genomes AF: 0.0485 AC: 7377 AN: 152048 Hom.: 266 Cov.: 32

Gnomad AFR AF: 0.0148

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0303

Gnomad ASJ AF: 0.0464

Gnomad EAS AF: 0.0929

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0997

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0574

Gnomad OTH AF: 0.0469

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0485 AC: 7381 AN: 152168 Hom.: 264 Cov.: 32 AF XY: 0.0515 AC XY: 3833 AN XY: 74394

Gnomad4 AFR AF: 0.0148

Gnomad4 AMR AF: 0.0302

Gnomad4 ASJ AF: 0.0464

Gnomad4 EAS AF: 0.0930

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0997

Gnomad4 NFE AF: 0.0574

Gnomad4 OTH AF: 0.0469

Alfa AF: 0.0575 Hom.: 148

Bravo AF: 0.0401

Asia WGS AF: 0.100 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.69
DANN	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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

Other links and lift over

dbSNP: rs13137332; hg19: chr4-183825036;