Genetic Variant DKK3:p.Glu307Gly (chr11-11964597-T-C) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001018057.2(DKK3):c.920A>G(p.Glu307Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00743 in 1,614,160 control chromosomes in the GnomAD database, including 175 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.019 ( 69 hom., cov: 33)

Exomes 𝑓: 0.0063 ( 106 hom. )

Consequence

DKK3
NM_001018057.2 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.29

Variant links:

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]

DKK3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0050218403).

BP6

Variant 11-11964597-T-C is Benign according to our data. Variant chr11-11964597-T-C is described in ClinVar as [Benign]. Clinvar id is 768428.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.053 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DKK3	NM_001018057.2 link	c.920A>G	p.Glu307Gly	missense_variant	Exon 7 of 7	ENST00000683431.1	NP_001018067.1	Q9UBP4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DKK3	ENST00000683431.1 link	c.920A>G	p.Glu307Gly	missense_variant	Exon 7 of 7		NM_001018057.2	ENSP00000506835.1		Q9UBP4

Frequencies

GnomAD3 genomes

AF:

0.0187

AC:

2845

AN:

152160

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0548

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0117

Gnomad ASJ

AF:

0.000865

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00973

Gnomad FIN

AF:

0.00113

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00443

Gnomad OTH

AF:

0.0129

GnomAD3 exomes

AF:

0.00845

AC:

2126

AN:

251454

Hom.:

AF XY:

0.00816

AC XY:

1109

AN XY:

135908

show subpopulations

Gnomad AFR exome

AF:

0.0568

Gnomad AMR exome

AF:

0.00517

Gnomad ASJ exome

AF:

0.00179

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.0131

Gnomad FIN exome

AF:

0.00106

Gnomad NFE exome

AF:

0.00469

Gnomad OTH exome

AF:

0.00782

GnomAD4 exome

AF:

0.00625

AC:

9139

AN:

1461882

Hom.:

106

Cov.:

AF XY:

0.00640

AC XY:

4653

AN XY:

727240

show subpopulations

Gnomad4 AFR exome

AF:

0.0565

Gnomad4 AMR exome

AF:

0.00615

Gnomad4 ASJ exome

AF:

0.00168

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.0130

Gnomad4 FIN exome

AF:

0.00114

Gnomad4 NFE exome

AF:

0.00462

Gnomad4 OTH exome

AF:

0.00836

GnomAD4 genome

AF:

0.0187

AC:

2854

AN:

152278

Hom.:

Cov.:

AF XY:

0.0184

AC XY:

1367

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.0549

Gnomad4 AMR

AF:

0.0117

Gnomad4 ASJ

AF:

0.000865

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00954

Gnomad4 FIN

AF:

0.00113

Gnomad4 NFE

AF:

0.00443

Gnomad4 OTH

AF:

0.0128

Alfa

AF:

0.00681

Hom.:

Bravo

AF:

0.0205

TwinsUK

AF:

0.00324

AC:

ALSPAC

AF:

0.00441

AC:

ESP6500AA

AF:

0.0566

AC:

249

ESP6500EA

AF:

0.00524

AC:

ExAC

AF:

0.00935

AC:

1135

Asia WGS

AF:

0.00808

AC:

AN:

3478

EpiCase

AF:

0.00545

EpiControl

AF:

0.00575

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 26, 2018

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.084

BayesDel_addAF

Benign

-0.65

BayesDel_noAF

Benign

-0.67

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.26

T;T;.

Eigen

Benign

-0.55

Eigen_PC

Benign

-0.57

FATHMM_MKL

Benign

0.46

LIST_S2

Benign

0.73

.;T;T

MetaRNN

Benign

0.0050

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

2.0

M;M;.

PrimateAI

Benign

0.29

PROVEAN

Benign

-1.6

N;N;N

REVEL

Benign

0.040

Sift

Uncertain

0.0050

D;D;D

Sift4G

Uncertain

0.037

D;D;D

Polyphen

0.65

P;P;P

Vest4

0.066

MVP

0.41

MPC

0.39

ClinPred

0.020

GERP RS

3.2

Varity_R

0.10

gMVP

0.52

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over