16-89686747-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001160367.2(CDK10):c.-139C>A variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,612,336 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_001160367.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152082Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000205 AC: 5AN: 244176Hom.: 0 AF XY: 0.0000300 AC XY: 4AN XY: 133282
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1460136Hom.: 0 Cov.: 31 AF XY: 0.00000964 AC XY: 7AN XY: 726370
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152200Hom.: 0 Cov.: 34 AF XY: 0.0000537 AC XY: 4AN XY: 74428
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.37C>A (p.L13M) alteration is located in exon 1 (coding exon 1) of the CDK10 gene. This alteration results from a C to A substitution at nucleotide position 37, causing the leucine (L) at amino acid position 13 to be replaced by a methionine (M). 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