rs7677967

Variant names:

• chr4-182889979-A-G
• rs7677967
• ENST00000795667.1:n.164-3618A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000795667.1(ENSG00000303565):​n.164-3618A>G variant causes a intron 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: ENSG00000303565 ENST00000795667.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.433
• Publications: 3 publications found

Genes affected

ENSG00000303565 (HGNC:):

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

Our verdict: Benign. The variant received -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	c.*1420T>C		downstream_gene_variant		ENST00000438320.7	NP_001912.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCTD	ENST00000438320.7	c.*1420T>C		downstream_gene_variant		1	NM_001921.3	ENSP00000398194.2

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54741 AN: 151990 Hom.: 12301 Cov.: 32

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: 1 AN: 12 Hom.: 0 AF XY: 0.100 AC XY: 1 AN XY: 10

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 6

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.360 AC: 54802 AN: 152108 Hom.: 12324 Cov.: 32 AF XY: 0.357 AC XY: 26514 AN XY: 74372

African (AFR) AF: 0.650 AC: 26965 AN: 41456

American (AMR) AF: 0.334 AC: 5103 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 753 AN: 3466

East Asian (EAS) AF: 0.268 AC: 1386 AN: 5172

South Asian (SAS) AF: 0.283 AC: 1362 AN: 4812

European-Finnish (FIN) AF: 0.210 AC: 2222 AN: 10594

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15941 AN: 67996

Other (OTH) AF: 0.334 AC: 705 AN: 2110

Alfa AF: 0.319 Hom.: 1254

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
PhyloP100		-0.43

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7677967; hg19: chr4-183811132;