Variant rs2308292 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_014421.3(DKK2):c.223-42670_223-42666delCTTAA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.38 ( 10872 hom., cov: 0)

Consequence

DKK2
NM_014421.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.05

Variant links:

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]

DKK2 links:

DKK2 (HGNC:):

DKK2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DKK2	NM_014421.3 linkuse as main transcript	c.223-42670_223-42666delCTTAA		intron_variant		ENST00000285311.8	NP_055236.1	Q9UBU2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
DKK2	ENST00000285311.8 linkuse as main transcript	c.223-42670_223-42666delCTTAA	intron_variant	1	NM_014421.3	ENSP00000285311.3	Q9UBU2
DKK2	ENST00000513208.5 linkuse as main transcript	c.-78-42670_-78-42666delCTTAA	intron_variant	1		ENSP00000421255.1	D6RGF1
DKK2	ENST00000510534.1 linkuse as main transcript	n.444-42670_444-42666delCTTAA	intron_variant	1
DKK2	ENST00000510463.1 linkuse as main transcript	c.85-42670_85-42666delCTTAA	intron_variant	3		ENSP00000423797.1	D6RCC2

Frequencies

GnomAD3 genomes

AF:

0.378

AC:

57364

AN:

151658

Hom.:

10865

Cov.:

show subpopulations

Gnomad AFR

AF:

0.444

Gnomad AMI

AF:

0.432

Gnomad AMR

AF:

0.340

Gnomad ASJ

AF:

0.349

Gnomad EAS

AF:

0.465

Gnomad SAS

AF:

0.262

Gnomad FIN

AF:

0.387

Gnomad MID

AF:

0.288

Gnomad NFE

AF:

0.348

Gnomad OTH

AF:

0.375

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

GnomAD4 genome

AF:

0.378

AC:

57412

AN:

151776

Hom.:

10872

Cov.:

AF XY:

0.378

AC XY:

28031

AN XY:

74162

show subpopulations

Gnomad4 AFR

AF:

0.444

Gnomad4 AMR

AF:

0.340

Gnomad4 ASJ

AF:

0.349

Gnomad4 EAS

AF:

0.465

Gnomad4 SAS

AF:

0.261

Gnomad4 FIN

AF:

0.387

Gnomad4 NFE

AF:

0.348

Gnomad4 OTH

AF:

0.381

Alfa

AF:

0.368

Hom.:

1272

Bravo

AF:

0.378

Asia WGS

AF:

0.367

AC:

1277

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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