10-52316299-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_012242.4(DKK1):āc.411A>Gā(p.Ile137Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,613,976 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 (ā ).
Frequency
Consequence
NM_012242.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DKK1 | ENST00000373970.4 | c.411A>G | p.Ile137Met | missense_variant | Exon 3 of 4 | 1 | NM_012242.4 | ENSP00000363081.3 | ||
DKK1 | ENST00000467359.5 | n.411A>G | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 | |||||
DKK1 | ENST00000476752.1 | n.60A>G | non_coding_transcript_exon_variant | Exon 2 of 3 | 2 | |||||
DKK1 | ENST00000494277.5 | n.34A>G | non_coding_transcript_exon_variant | Exon 2 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251234Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135784
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461754Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727164
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152222Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.411A>G (p.I137M) alteration is located in exon 3 (coding exon 3) of the DKK1 gene. This alteration results from a A to G substitution at nucleotide position 411, causing the isoleucine (I) at amino acid position 137 to be replaced by a methionine (M). 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