10-52316420-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_012242.4(DKK1):āc.532A>Cā(p.Met178Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,818 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 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 -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DKK1 | ENST00000373970.4 | c.532A>C | p.Met178Leu | missense_variant | Exon 3 of 4 | 1 | NM_012242.4 | ENSP00000363081.3 | ||
DKK1 | ENST00000467359.5 | n.532A>C | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 | |||||
DKK1 | ENST00000476752.1 | n.181A>C | non_coding_transcript_exon_variant | Exon 2 of 3 | 2 | |||||
DKK1 | ENST00000494277.5 | n.155A>C | non_coding_transcript_exon_variant | Exon 2 of 4 | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461818Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727200
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.532A>C (p.M178L) alteration is located in exon 3 (coding exon 3) of the DKK1 gene. This alteration results from a A to C substitution at nucleotide position 532, causing the methionine (M) at amino acid position 178 to be replaced by a leucine (L). 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