rs2073664
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_014420.3(DKK4):c.507C>T(p.Val169=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 1,613,456 control chromosomes in the GnomAD database, including 21,910 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 0.24 ( 8417 hom., cov: 32)
Exomes 𝑓: 0.098 ( 13493 hom. )
Consequence
DKK4
NM_014420.3 synonymous
NM_014420.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.316
Genes affected
DKK4 (HGNC:2894): (dickkopf WNT signaling pathway inhibitor 4) 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. Activity of this protein is modulated by binding to the Wnt co-receptor and the co-factor kremen 2. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP7
?
Synonymous conserved (PhyloP=0.316 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DKK4 | NM_014420.3 | c.507C>T | p.Val169= | synonymous_variant | 4/4 | ENST00000220812.3 | |
DKK4 | XM_011544488.3 | c.507C>T | p.Val169= | synonymous_variant | 5/5 | ||
DKK4 | XM_017013316.2 | c.507C>T | p.Val169= | synonymous_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DKK4 | ENST00000220812.3 | c.507C>T | p.Val169= | synonymous_variant | 4/4 | 1 | NM_014420.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.238 AC: 36098AN: 151788Hom.: 8383 Cov.: 32
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GnomAD3 exomes AF: 0.137 AC: 34467AN: 251080Hom.: 4866 AF XY: 0.132 AC XY: 17902AN XY: 135714
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GnomAD4 exome AF: 0.0981 AC: 143410AN: 1461550Hom.: 13493 Cov.: 32 AF XY: 0.0997 AC XY: 72463AN XY: 727082
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GnomAD4 genome ? AF: 0.238 AC: 36175AN: 151906Hom.: 8417 Cov.: 32 AF XY: 0.240 AC XY: 17829AN XY: 74252
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at