rs201507040
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The NM_001160367.2(CDK10):c.-127+2T>C variant causes a splice donor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,612,238 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001160367.2 splice_donor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151906Hom.: 0 Cov.: 34
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460332Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726474
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151906Hom.: 0 Cov.: 34 AF XY: 0.0000135 AC XY: 1AN XY: 74200
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at