chr17-62479511-T-TGGGGCCG
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_006852.6(TLK2):c.-6+223_-6+229dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000343 in 151,816 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00034 ( 0 hom., cov: 32)
Consequence
TLK2
NM_006852.6 intron
NM_006852.6 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.05
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 -9 ACMG points.
BP6
?
Variant 17-62479511-T-TGGGGCCG is Benign according to our data. Variant chr17-62479511-T-TGGGGCCG is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 1694856.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Likely_benign=1}.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000343 (52/151816) while in subpopulation EAS AF= 0.0053 (27/5094). AF 95% confidence interval is 0.00374. There are 0 homozygotes in gnomad4. There are 31 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 52 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TLK2 | NM_006852.6 | c.-6+223_-6+229dup | intron_variant | ENST00000346027.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLK2 | ENST00000346027.10 | c.-6+223_-6+229dup | intron_variant | 1 | NM_006852.6 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.000343 AC: 52AN: 151704Hom.: 0 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.000343 AC: 52AN: 151816Hom.: 0 Cov.: 32 AF XY: 0.000418 AC XY: 31AN XY: 74232
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Intellectual disability, autosomal dominant 57 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | MGZ Medical Genetics Center | Sep 03, 2021 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | TLK2: BS1 - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at