10-52316340-A-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_012242.4(DKK1):c.452A>T(p.Glu151Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000112 in 1,614,168 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_012242.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DKK1 | ENST00000373970.4 | c.452A>T | p.Glu151Val | missense_variant | Exon 3 of 4 | 1 | NM_012242.4 | ENSP00000363081.3 | ||
DKK1 | ENST00000467359.5 | n.452A>T | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 | |||||
DKK1 | ENST00000476752.1 | n.101A>T | non_coding_transcript_exon_variant | Exon 2 of 3 | 2 | |||||
DKK1 | ENST00000494277.5 | n.75A>T | non_coding_transcript_exon_variant | Exon 2 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251378Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135864
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461846Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727218
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152322Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.452A>T (p.E151V) alteration is located in exon 3 (coding exon 3) of the DKK1 gene. This alteration results from a A to T substitution at nucleotide position 452, causing the glutamic acid (E) at amino acid position 151 to be replaced by a valine (V). 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