17-62479268-AGCGGCGGCGGCG-AGCGGCG
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_006852.6(TLK2):c.-13_-8delGGCGGC variant causes a splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00014 in 150,516 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00014 ( 0 hom., 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: 2.27
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 Benign. Variant got -8 ACMG points.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00014 (21/150516) while in subpopulation AFR AF= 0.00039 (16/40978). AF 95% confidence interval is 0.000244. There are 0 homozygotes in gnomad4. There are 8 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High AC in GnomAd4 at 21 AD gene.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TLK2 | ENST00000346027.10 | c.-13_-8delGGCGGC | splice_region_variant | Exon 1 of 22 | 1 | NM_006852.6 | ENSP00000275780.7 | |||
TLK2 | ENST00000346027 | c.-13_-8delGGCGGC | 5_prime_UTR_variant | Exon 1 of 22 | 1 | NM_006852.6 | ENSP00000275780.7 |
Frequencies
GnomAD3 genomes AF: 0.000140 AC: 21AN: 150516Hom.: 0 Cov.: 31
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GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 15940Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 11902
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GnomAD4 genome AF: 0.000140 AC: 21AN: 150516Hom.: 0 Cov.: 31 AF XY: 0.000109 AC XY: 8AN XY: 73456
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ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at