10-52315016-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_012242.4(DKK1):c.337G>A(p.Ala113Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000231 in 1,605,056 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 Conflicting classifications of pathogenicity (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 -7 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DKK1 | ENST00000373970.4 | c.337G>A | p.Ala113Thr | missense_variant | Exon 2 of 4 | 1 | NM_012242.4 | ENSP00000363081.3 | ||
DKK1 | ENST00000467359.5 | n.337G>A | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 | |||||
DKK1 | ENST00000494277.5 | n.-41G>A | upstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152014Hom.: 0 Cov.: 27
GnomAD3 exomes AF: 0.0000202 AC: 5AN: 247324Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 134000
GnomAD4 exome AF: 0.0000165 AC: 24AN: 1453042Hom.: 0 Cov.: 35 AF XY: 0.0000153 AC XY: 11AN XY: 721228
GnomAD4 genome AF: 0.0000855 AC: 13AN: 152014Hom.: 0 Cov.: 27 AF XY: 0.000121 AC XY: 9AN XY: 74238
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.337G>A (p.A113T) alteration is located in exon 2 (coding exon 2) of the DKK1 gene. This alteration results from a G to A substitution at nucleotide position 337, causing the alanine (A) at amino acid position 113 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not provided Benign:1
DKK1: BP4 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at