10-52316550-G-A

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_012242.4(DKK1):​c.548-4G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00327 in 1,613,576 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0038 ( 6 hom., cov: 33)
Exomes 𝑓: 0.0032 ( 12 hom. )

Consequence

DKK1
NM_012242.4 splice_region, intron

Scores

2
Splicing: ADA: 0.00001591
2

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.16
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 -16 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 10-52316550-G-A is Benign according to our data. Variant chr10-52316550-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 773234.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High AC in GnomAd4 at 571 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DKK1NM_012242.4 linkc.548-4G>A splice_region_variant, intron_variant Intron 3 of 3 ENST00000373970.4 NP_036374.1 O94907I1W660

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DKK1ENST00000373970.4 linkc.548-4G>A splice_region_variant, intron_variant Intron 3 of 3 1 NM_012242.4 ENSP00000363081.3 O94907
DKK1ENST00000476752.1 linkn.197-4G>A splice_region_variant, intron_variant Intron 2 of 2 2
DKK1ENST00000494277.5 linkn.171-4G>A splice_region_variant, intron_variant Intron 2 of 3 5

Frequencies

GnomAD3 genomes
AF:
0.00375
AC:
571
AN:
152078
Hom.:
6
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000580
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000196
Gnomad ASJ
AF:
0.00346
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.0145
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00550
Gnomad OTH
AF:
0.00191
GnomAD3 exomes
AF:
0.00355
AC:
890
AN:
250922
Hom.:
2
AF XY:
0.00358
AC XY:
485
AN XY:
135590
show subpopulations
Gnomad AFR exome
AF:
0.000677
Gnomad AMR exome
AF:
0.000377
Gnomad ASJ exome
AF:
0.00258
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.0136
Gnomad NFE exome
AF:
0.00467
Gnomad OTH exome
AF:
0.00262
GnomAD4 exome
AF:
0.00322
AC:
4704
AN:
1461380
Hom.:
12
Cov.:
33
AF XY:
0.00329
AC XY:
2389
AN XY:
726946
show subpopulations
Gnomad4 AFR exome
AF:
0.000329
Gnomad4 AMR exome
AF:
0.000582
Gnomad4 ASJ exome
AF:
0.00280
Gnomad4 EAS exome
AF:
0.000126
Gnomad4 SAS exome
AF:
0.0000580
Gnomad4 FIN exome
AF:
0.0141
Gnomad4 NFE exome
AF:
0.00329
Gnomad4 OTH exome
AF:
0.00295
GnomAD4 genome
AF:
0.00375
AC:
571
AN:
152196
Hom.:
6
Cov.:
33
AF XY:
0.00388
AC XY:
289
AN XY:
74410
show subpopulations
Gnomad4 AFR
AF:
0.000578
Gnomad4 AMR
AF:
0.000196
Gnomad4 ASJ
AF:
0.00346
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.0145
Gnomad4 NFE
AF:
0.00550
Gnomad4 OTH
AF:
0.00189
Alfa
AF:
0.00428
Hom.:
2
Bravo
AF:
0.00206
EpiCase
AF:
0.00311
EpiControl
AF:
0.00290

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Nov 01, 2024
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

DKK1: BP4, BS2 -

Jul 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
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.4
DANN
Benign
0.70
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.000016
dbscSNV1_RF
Benign
0.012
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: rs183951849; hg19: chr10-54076310; API