chr11-11962338-C-T

Variant names:

• chr11-11962338-C-T
• rs1472189
• ENST00000396505:c.*2126G>A

Variant summary

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

The ENST00000396505(DKK3):​c.*2126G>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 0.249 in 152,046 control chromosomes in the GnomAD database, including 5,474 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 0.25 (5474 hom., cov: 32)
• Consequence: DKK3 ENST00000396505 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365

Genes affected

DKK3 (HGNC:2893): (dickkopf WNT signaling pathway inhibitor 3) This gene encodes a protein that is a member of the dickkopf family. The secreted protein contains two cysteine rich regions and is involved in embryonic development through its interactions with the Wnt signaling pathway. The expression of this gene is decreased in a variety of cancer cell lines and it may function as a tumor suppressor gene. Alternative splicing results in multiple transcript variants encoding the same protein. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DKK3	ENST00000396505	c.*2126G>A		3_prime_UTR_variant	Exon 8 of 8	1		ENSP00000379762.2

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37853 AN: 151928 Hom.: 5476 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.249 AC: 37853 AN: 152046 Hom.: 5474 Cov.: 32 AF XY: 0.250 AC XY: 18544 AN XY: 74294

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.281

Alfa AF: 0.302 Hom.: 7092

Bravo AF: 0.241

Asia WGS AF: 0.227 AC: 786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1472189; hg19: chr11-11983885;