10-52314917-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_012242.4(DKK1):c.244-6C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000379 in 1,509,944 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Benign (★★).
Frequency
Consequence
NM_012242.4 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00218 AC: 331AN: 152032Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000672 AC: 100AN: 148708Hom.: 0 AF XY: 0.000562 AC XY: 44AN XY: 78298
GnomAD4 exome AF: 0.000178 AC: 242AN: 1357794Hom.: 0 Cov.: 31 AF XY: 0.000152 AC XY: 101AN XY: 663004
GnomAD4 genome AF: 0.00218 AC: 331AN: 152150Hom.: 0 Cov.: 31 AF XY: 0.00208 AC XY: 155AN XY: 74366
ClinVar
Submissions by phenotype
not provided Benign:2
- -
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at