rs141115379

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_012242.4(DKK1):​c.316G>A​(p.Ala106Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00144 in 1,604,536 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0020 ( 2 hom., cov: 31)
Exomes 𝑓: 0.0014 ( 4 hom. )

Consequence

DKK1
NM_012242.4 missense

Scores

19

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.261
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 -10 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0057531).
BP6
Variant 10-52314995-G-A is Benign according to our data. Variant chr10-52314995-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2640477.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 308 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DKK1NM_012242.4 linkc.316G>A p.Ala106Thr 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.316G>A p.Ala106Thr missense_variant Exon 2 of 4 1 NM_012242.4 ENSP00000363081.3 O94907
DKK1ENST00000467359.5 linkn.316G>A non_coding_transcript_exon_variant Exon 1 of 2 2

Frequencies

GnomAD3 genomes
AF:
0.00203
AC:
308
AN:
152068
Hom.:
2
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0000966
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000196
Gnomad ASJ
AF:
0.00115
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00726
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.00318
Gnomad OTH
AF:
0.00143
GnomAD3 exomes
AF:
0.00193
AC:
477
AN:
246790
Hom.:
2
AF XY:
0.00193
AC XY:
258
AN XY:
133774
show subpopulations
Gnomad AFR exome
AF:
0.000187
Gnomad AMR exome
AF:
0.000117
Gnomad ASJ exome
AF:
0.00182
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00651
Gnomad NFE exome
AF:
0.00272
Gnomad OTH exome
AF:
0.00182
GnomAD4 exome
AF:
0.00138
AC:
2002
AN:
1452350
Hom.:
4
Cov.:
31
AF XY:
0.00141
AC XY:
1016
AN XY:
720696
show subpopulations
Gnomad4 AFR exome
AF:
0.0000601
Gnomad4 AMR exome
AF:
0.000135
Gnomad4 ASJ exome
AF:
0.00204
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00751
Gnomad4 NFE exome
AF:
0.00131
Gnomad4 OTH exome
AF:
0.00160
GnomAD4 genome
AF:
0.00202
AC:
308
AN:
152186
Hom.:
2
Cov.:
31
AF XY:
0.00203
AC XY:
151
AN XY:
74408
show subpopulations
Gnomad4 AFR
AF:
0.0000963
Gnomad4 AMR
AF:
0.000196
Gnomad4 ASJ
AF:
0.00115
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00726
Gnomad4 NFE
AF:
0.00318
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.00307
Hom.:
2
Bravo
AF:
0.000945
TwinsUK
AF:
0.00
AC:
0
ALSPAC
AF:
0.000778
AC:
3
ESP6500AA
AF:
0.000227
AC:
1
ESP6500EA
AF:
0.000698
AC:
6
ExAC
AF:
0.00212
AC:
257
EpiCase
AF:
0.00126
EpiControl
AF:
0.00143

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Jul 01, 2022
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

DKK1: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.065
BayesDel_addAF
Benign
-0.66
T
BayesDel_noAF
Benign
-0.72
CADD
Benign
16
DANN
Benign
0.97
DEOGEN2
Benign
0.38
T
Eigen
Benign
-0.95
Eigen_PC
Benign
-0.93
FATHMM_MKL
Benign
0.38
N
LIST_S2
Benign
0.53
T
M_CAP
Benign
0.0053
T
MetaRNN
Benign
0.0058
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.41
N
PrimateAI
Benign
0.40
T
PROVEAN
Benign
-0.65
N
REVEL
Benign
0.038
Sift
Benign
0.090
T
Sift4G
Benign
0.56
T
Polyphen
0.0010
B
Vest4
0.12
MVP
0.43
MPC
0.44
ClinPred
0.0073
T
GERP RS
1.1
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.044
gMVP
0.55

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.11
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: rs141115379; hg19: chr10-54074755; COSMIC: COSV64760618; COSMIC: COSV64760618; API