rs10021344
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014421.3(DKK2):c.222+5167C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 151,786 control chromosomes in the GnomAD database, including 11,949 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.37 ( 11949 hom., cov: 33)
Consequence
DKK2
NM_014421.3 intron
NM_014421.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.530
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DKK2 | NM_014421.3 | c.222+5167C>T | intron_variant | ENST00000285311.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DKK2 | ENST00000285311.8 | c.222+5167C>T | intron_variant | 1 | NM_014421.3 | P1 | |||
DKK2 | ENST00000513208.5 | c.-78-104254C>T | intron_variant | 1 | |||||
DKK2 | ENST00000510534.1 | n.443+5167C>T | intron_variant, non_coding_transcript_variant | 1 | |||||
DKK2 | ENST00000510463.1 | c.84+97739C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.374 AC: 56662AN: 151668Hom.: 11952 Cov.: 33
GnomAD3 genomes
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.373 AC: 56662AN: 151786Hom.: 11949 Cov.: 33 AF XY: 0.364 AC XY: 26970AN XY: 74178
GnomAD4 genome
?
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56662
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151786
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33
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26970
AN XY:
74178
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427
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3476
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at