17-62479268-AGCGGCGGCGGCG-AGCGGCGGCGGCGGCGGCGGCG
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_006852.6(TLK2):c.-16_-8dupGGCGGCGGC variant causes a splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000408 in 166,558 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00039 ( 1 hom., cov: 31)
Exomes 𝑓: 0.00056 ( 0 hom. )
Consequence
TLK2
NM_006852.6 splice_region
NM_006852.6 splice_region
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.343
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 sas. gnomad4 allele frequency = 0.000392 (59/150616) while in subpopulation SAS AF= 0.000834 (4/4798). AF 95% confidence interval is 0.000435. There are 1 homozygotes in gnomad4. There are 28 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High AC in GnomAd4 at 59 AD gene.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TLK2 | ENST00000346027.10 | c.-16_-8dupGGCGGCGGC | splice_region_variant | Exon 1 of 22 | 1 | NM_006852.6 | ENSP00000275780.7 | |||
TLK2 | ENST00000346027 | c.-16_-8dupGGCGGCGGC | 5_prime_UTR_variant | Exon 1 of 22 | 1 | NM_006852.6 | ENSP00000275780.7 |
Frequencies
GnomAD3 genomes AF: 0.000392 AC: 59AN: 150516Hom.: 1 Cov.: 31
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GnomAD4 exome AF: 0.000565 AC: 9AN: 15942Hom.: 0 Cov.: 0 AF XY: 0.000420 AC XY: 5AN XY: 11904
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GnomAD4 genome AF: 0.000392 AC: 59AN: 150616Hom.: 1 Cov.: 31 AF XY: 0.000381 AC XY: 28AN XY: 73564
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ClinVar
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at