10-52315038-G-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_012242.4(DKK1):​c.359G>T​(p.Arg120Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00317 in 1,603,066 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.0027 ( 1 hom., cov: 26)
Exomes 𝑓: 0.0032 ( 9 hom. )

Consequence

DKK1
NM_012242.4 missense

Scores

9
6
4

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 9.49
Variant links:
Genes affected
DKK1 (HGNC:2891): (dickkopf WNT signaling pathway inhibitor 1) This gene encodes a member of the dickkopf family of proteins. Members of this family are secreted proteins characterized by two cysteine-rich domains that mediate protein-protein interactions. The encoded protein binds to the LRP6 co-receptor and inhibits beta-catenin-dependent Wnt signaling. This gene plays a role in embryonic development and may be important in bone formation in adults. Elevated expression of this gene has been observed in numerous human cancers and this protein may promote proliferation, invasion and growth in cancer cell lines. [provided by RefSeq, Sep 2017]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.03161475).
BS2
High AC in GnomAd4 at 403 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DKK1NM_012242.4 linkc.359G>T p.Arg120Leu missense_variant Exon 2 of 4 ENST00000373970.4 NP_036374.1 O94907I1W660

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DKK1ENST00000373970.4 linkc.359G>T p.Arg120Leu missense_variant Exon 2 of 4 1 NM_012242.4 ENSP00000363081.3 O94907
DKK1ENST00000467359.5 linkn.359G>T non_coding_transcript_exon_variant Exon 1 of 2 2
DKK1ENST00000494277.5 linkn.-19G>T upstream_gene_variant 5

Frequencies

GnomAD3 genomes
AF:
0.00265
AC:
402
AN:
151932
Hom.:
1
Cov.:
26
show subpopulations
Gnomad AFR
AF:
0.000725
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00282
Gnomad ASJ
AF:
0.00173
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000625
Gnomad FIN
AF:
0.00179
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.00437
Gnomad OTH
AF:
0.000958
GnomAD3 exomes
AF:
0.00286
AC:
701
AN:
244824
Hom.:
1
AF XY:
0.00302
AC XY:
400
AN XY:
132628
show subpopulations
Gnomad AFR exome
AF:
0.000622
Gnomad AMR exome
AF:
0.00192
Gnomad ASJ exome
AF:
0.00260
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00101
Gnomad FIN exome
AF:
0.00228
Gnomad NFE exome
AF:
0.00458
Gnomad OTH exome
AF:
0.00303
GnomAD4 exome
AF:
0.00323
AC:
4681
AN:
1451016
Hom.:
9
Cov.:
35
AF XY:
0.00323
AC XY:
2328
AN XY:
720224
show subpopulations
Gnomad4 AFR exome
AF:
0.000663
Gnomad4 AMR exome
AF:
0.00202
Gnomad4 ASJ exome
AF:
0.00194
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000938
Gnomad4 FIN exome
AF:
0.00265
Gnomad4 NFE exome
AF:
0.00367
Gnomad4 OTH exome
AF:
0.00351
GnomAD4 genome
AF:
0.00265
AC:
403
AN:
152050
Hom.:
1
Cov.:
26
AF XY:
0.00271
AC XY:
201
AN XY:
74296
show subpopulations
Gnomad4 AFR
AF:
0.000723
Gnomad4 AMR
AF:
0.00281
Gnomad4 ASJ
AF:
0.00173
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000625
Gnomad4 FIN
AF:
0.00179
Gnomad4 NFE
AF:
0.00438
Gnomad4 OTH
AF:
0.000948
Alfa
AF:
0.00403
Hom.:
3
Bravo
AF:
0.00246
TwinsUK
AF:
0.00431
AC:
16
ALSPAC
AF:
0.00415
AC:
16
ESP6500AA
AF:
0.000681
AC:
3
ESP6500EA
AF:
0.00430
AC:
37
ExAC
AF:
0.00291
AC:
353
Asia WGS
AF:
0.000577
AC:
2
AN:
3478

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

DKK1-related disorder Benign:1
Dec 28, 2022
PreventionGenetics, part of Exact Sciences
Significance: Likely benign
Review Status: no assertion criteria provided
Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.89
BayesDel_addAF
Benign
-0.0028
T
BayesDel_noAF
Pathogenic
0.22
CADD
Pathogenic
33
DANN
Uncertain
1.0
DEOGEN2
Pathogenic
0.88
D
Eigen
Pathogenic
0.93
Eigen_PC
Pathogenic
0.91
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.94
D
M_CAP
Uncertain
0.11
D
MetaRNN
Benign
0.032
T
MetaSVM
Benign
-0.28
T
MutationAssessor
Uncertain
2.6
M
PrimateAI
Uncertain
0.69
T
PROVEAN
Pathogenic
-6.2
D
REVEL
Uncertain
0.63
Sift
Pathogenic
0.0
D
Sift4G
Pathogenic
0.0
D
Polyphen
1.0
D
Vest4
0.87
MVP
0.85
MPC
1.5
ClinPred
0.038
T
GERP RS
5.6
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.87
gMVP
0.86

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.

Other links and lift over

dbSNP: rs149268042; hg19: chr10-54074798; COSMIC: COSV100906470; COSMIC: COSV100906470; API