10-52315038-G-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_012242.4(DKK1):c.359G>T(p.Arg120Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00317 in 1,603,066 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_012242.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DKK1 | ENST00000373970.4 | c.359G>T | p.Arg120Leu | missense_variant | Exon 2 of 4 | 1 | NM_012242.4 | ENSP00000363081.3 | ||
DKK1 | ENST00000467359.5 | n.359G>T | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 | |||||
DKK1 | ENST00000494277.5 | n.-19G>T | upstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00265 AC: 402AN: 151932Hom.: 1 Cov.: 26
GnomAD3 exomes AF: 0.00286 AC: 701AN: 244824Hom.: 1 AF XY: 0.00302 AC XY: 400AN XY: 132628
GnomAD4 exome AF: 0.00323 AC: 4681AN: 1451016Hom.: 9 Cov.: 35 AF XY: 0.00323 AC XY: 2328AN XY: 720224
GnomAD4 genome AF: 0.00265 AC: 403AN: 152050Hom.: 1 Cov.: 26 AF XY: 0.00271 AC XY: 201AN XY: 74296
ClinVar
Submissions by phenotype
DKK1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at