NM_012242.4:c.556G>T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_012242.4(DKK1):c.556G>T(p.Gly186Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000589 in 1,613,834 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_012242.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DKK1 | ENST00000373970.4 | c.556G>T | p.Gly186Cys | missense_variant | Exon 4 of 4 | 1 | NM_012242.4 | ENSP00000363081.3 | ||
DKK1 | ENST00000476752.1 | n.205G>T | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 | |||||
DKK1 | ENST00000494277.5 | n.179G>T | non_coding_transcript_exon_variant | Exon 3 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251102Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135704
GnomAD4 exome AF: 0.0000623 AC: 91AN: 1461652Hom.: 0 Cov.: 32 AF XY: 0.0000633 AC XY: 46AN XY: 727108
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152182Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.556G>T (p.G186C) alteration is located in exon 4 (coding exon 4) of the DKK1 gene. This alteration results from a G to T substitution at nucleotide position 556, causing the glycine (G) at amino acid position 186 to be replaced by a cysteine (C). 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