rs10488899

chr4-106943654-T-G

Variant summary

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

The NM_014421.3(DKK2):c.223-17705A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,106 control chromosomes in the GnomAD database, including 1,867 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 0.13 (1867 hom., cov: 32)
• Consequence: DKK2 NM_014421.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500

Genes affected

DKK2 (HGNC:2892): (dickkopf WNT signaling pathway inhibitor 2) 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. It can act as either an agonist or antagonist of Wnt/beta-catenin signaling, depending on the cellular context and the presence of the co-factor kremen 2. Activity of this protein is also modulated by binding to the Wnt co-receptor LDL-receptor related protein 6 (LRP6). [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 = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DKK2	NM_014421.3	c.223-17705A>C		intron_variant		ENST00000285311.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DKK2	ENST00000285311.8	c.223-17705A>C		intron_variant		1	NM_014421.3	P1
DKK2	ENST00000513208.5	c.-78-17705A>C		intron_variant		1
DKK2	ENST00000510534.1	n.444-17705A>C		intron_variant, non_coding_transcript_variant		1
DKK2	ENST00000510463.1	c.85-17705A>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20316 AN: 151988 Hom.: 1866 Cov.: 32

Gnomad AFR AF: 0.0325

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.134 AC: 20312 AN: 152106 Hom.: 1867 Cov.: 32 AF XY: 0.131 AC XY: 9716 AN XY: 74362

Gnomad4 AFR AF: 0.0324

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.145

Alfa AF: 0.190 Hom.: 5849

Bravo AF: 0.127

Asia WGS AF: 0.0490 AC: 172 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	0.27
Dann	Benign	0.73

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

Other links and lift over

dbSNP: rs10488899; hg19: chr4-107864811;