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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.27
Variant links:
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]

Genome browser will be placed here

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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TLK2NM_006852.6 linkc.-13_-8delGGCGGC splice_region_variant Exon 1 of 22 ENST00000346027.10 NP_006843.2 Q86UE8-2
TLK2NM_006852.6 linkc.-13_-8delGGCGGC 5_prime_UTR_variant Exon 1 of 22 ENST00000346027.10 NP_006843.2 Q86UE8-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TLK2ENST00000346027.10 linkc.-13_-8delGGCGGC splice_region_variant Exon 1 of 22 1 NM_006852.6 ENSP00000275780.7 Q86UE8-2
TLK2ENST00000346027 linkc.-13_-8delGGCGGC 5_prime_UTR_variant Exon 1 of 22 1 NM_006852.6 ENSP00000275780.7 Q86UE8-2

Frequencies

GnomAD3 genomes
AF:
0.000140
AC:
21
AN:
150516
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.000390
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.0000967
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000445
Gnomad OTH
AF:
0.000482
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
15940
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
11902
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.000140
AC:
21
AN:
150516
Hom.:
0
Cov.:
31
AF XY:
0.000109
AC XY:
8
AN XY:
73456
show subpopulations
Gnomad4 AFR
AF:
0.000390
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.0000967
Gnomad4 NFE
AF:
0.0000445
Gnomad4 OTH
AF:
0.000482
Bravo
AF:
0.000128

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs768508482; hg19: chr17-60556629; API