15-74615677-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003992.5(CLK3):c.1-3520C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000242 in 1,242,016 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_003992.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLK3 | NM_003992.5 | c.1-3520C>T | intron_variant | Intron 1 of 12 | NP_003983.2 | |||
LOC102723750 | XR_007064714.1 | n.116G>A | non_coding_transcript_exon_variant | Exon 1 of 12 | ||||
LOC102723750 | XR_007064715.1 | n.116G>A | non_coding_transcript_exon_variant | Exon 1 of 9 | ||||
CLK3 | NM_001130028.2 | c.-222C>T | upstream_gene_variant | ENST00000395066.9 | NP_001123500.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152182Hom.: 0 Cov.: 33
GnomAD4 exome AF: 9.18e-7 AC: 1AN: 1089834Hom.: 0 Cov.: 30 AF XY: 0.00000194 AC XY: 1AN XY: 516322
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152182Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.223C>T (p.L75F) alteration is located in exon 1 (coding exon 1) of the CLK3 gene. This alteration results from a C to T substitution at nucleotide position 223, causing the leucine (L) at amino acid position 75 to be replaced by a phenylalanine (F). 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