10-52314971-G-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_012242.4(DKK1):āc.292G>Cā(p.Ala98Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000706 in 1,600,892 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (ā ).
Frequency
Consequence
NM_012242.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152062Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000496 AC: 12AN: 242118Hom.: 0 AF XY: 0.0000610 AC XY: 8AN XY: 131248
GnomAD4 exome AF: 0.0000745 AC: 108AN: 1448830Hom.: 0 Cov.: 31 AF XY: 0.0000877 AC XY: 63AN XY: 718478
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152062Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74266
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.292G>C (p.A98P) alteration is located in exon 2 (coding exon 2) of the DKK1 gene. This alteration results from a G to C substitution at nucleotide position 292, causing the alanine (A) at amino acid position 98 to be replaced by a proline (P). 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