11-11965933-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001018057.2(DKK3):c.706G>A(p.Val236Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000545 in 1,613,592 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001018057.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152212Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000120 AC: 30AN: 249132Hom.: 0 AF XY: 0.000156 AC XY: 21AN XY: 134876
GnomAD4 exome AF: 0.0000479 AC: 70AN: 1461262Hom.: 1 Cov.: 31 AF XY: 0.0000578 AC XY: 42AN XY: 726932
GnomAD4 genome AF: 0.000118 AC: 18AN: 152330Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.706G>A (p.V236M) alteration is located in exon 7 (coding exon 6) of the DKK3 gene. This alteration results from a G to A substitution at nucleotide position 706, causing the valine (V) at amino acid position 236 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at