NM_006852.6:c.-19_-8delGGCGGCGGCGGC
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006852.6(TLK2):c.-19_-8delGGCGGCGGCGGC variant causes a splice region change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
TLK2
NM_006852.6 splice_region
NM_006852.6 splice_region
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.87
Genes affected
TLK2 (HGNC:11842): (tousled like kinase 2) This gene encodes a nuclear serine/threonine kinase that was first identified in Arabidopsis. The encoded protein is thought to function in the regulation of chromatin assembly in the S phase of the cell cycle by regulating the levels of a histone H3/H4 chaperone. This protein is associated with double-strand break repair of DNA damage caused by radiation. Pseudogenes of this gene are present on chromosomes 10 and 17. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TLK2 | NM_006852.6 | c.-19_-8delGGCGGCGGCGGC | splice_region_variant | Exon 1 of 22 | ENST00000346027.10 | NP_006843.2 | ||
TLK2 | NM_006852.6 | c.-19_-8delGGCGGCGGCGGC | 5_prime_UTR_variant | Exon 1 of 22 | ENST00000346027.10 | NP_006843.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TLK2 | ENST00000346027.10 | c.-19_-8delGGCGGCGGCGGC | splice_region_variant | Exon 1 of 22 | 1 | NM_006852.6 | ENSP00000275780.7 | |||
TLK2 | ENST00000346027 | c.-19_-8delGGCGGCGGCGGC | 5_prime_UTR_variant | Exon 1 of 22 | 1 | NM_006852.6 | ENSP00000275780.7 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 15942Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 11904
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
15942
Hom.:
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0
AN XY:
11904
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GnomAD4 genome Cov.: 31
GnomAD4 genome
Cov.:
31
Bravo
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at