rs141115379
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_012242.4(DKK1):c.316G>A(p.Ala106Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00144 in 1,604,536 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_012242.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00203 AC: 308AN: 152068Hom.: 2 Cov.: 31
GnomAD3 exomes AF: 0.00193 AC: 477AN: 246790Hom.: 2 AF XY: 0.00193 AC XY: 258AN XY: 133774
GnomAD4 exome AF: 0.00138 AC: 2002AN: 1452350Hom.: 4 Cov.: 31 AF XY: 0.00141 AC XY: 1016AN XY: 720696
GnomAD4 genome AF: 0.00202 AC: 308AN: 152186Hom.: 2 Cov.: 31 AF XY: 0.00203 AC XY: 151AN XY: 74408
ClinVar
Submissions by phenotype
not provided Benign:1
DKK1: BP4, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at