10-52316550-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_012242.4(DKK1):c.548-4G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00327 in 1,613,576 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_012242.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DKK1 | ENST00000373970.4 | c.548-4G>A | splice_region_variant, intron_variant | Intron 3 of 3 | 1 | NM_012242.4 | ENSP00000363081.3 | |||
DKK1 | ENST00000476752.1 | n.197-4G>A | splice_region_variant, intron_variant | Intron 2 of 2 | 2 | |||||
DKK1 | ENST00000494277.5 | n.171-4G>A | splice_region_variant, intron_variant | Intron 2 of 3 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00375 AC: 571AN: 152078Hom.: 6 Cov.: 33
GnomAD3 exomes AF: 0.00355 AC: 890AN: 250922Hom.: 2 AF XY: 0.00358 AC XY: 485AN XY: 135590
GnomAD4 exome AF: 0.00322 AC: 4704AN: 1461380Hom.: 12 Cov.: 33 AF XY: 0.00329 AC XY: 2389AN XY: 726946
GnomAD4 genome AF: 0.00375 AC: 571AN: 152196Hom.: 6 Cov.: 33 AF XY: 0.00388 AC XY: 289AN XY: 74410
ClinVar
Submissions by phenotype
not provided Benign:2
DKK1: BP4, BS2 -
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at