11-11965906-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.733G>A(p.Ala245Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,614,036 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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: 0.0000263 AC: 4AN: 152178Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250604Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135584
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461740Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727174
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152296Hom.: 0 Cov.: 33 AF XY: 0.0000940 AC XY: 7AN XY: 74464
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.733G>A (p.A245T) 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 733, causing the alanine (A) at amino acid position 245 to be replaced by a threonine (T). 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