rs725131
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000569718.6(TK2):c.-351-89G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,150 control chromosomes in the GnomAD database, including 7,212 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.25 ( 7212 hom., cov: 33)
Exomes 𝑓: 0.12 ( 0 hom. )
Consequence
TK2
ENST00000569718.6 intron
ENST00000569718.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.275
Genes affected
TK2 (HGNC:11831): (thymidine kinase 2) This gene encodes a deoxyribonucleoside kinase that specifically phosphorylates thymidine, deoxycytidine, and deoxyuridine. The encoded enzyme localizes to the mitochondria and is required for mitochondrial DNA synthesis. Mutations in this gene are associated with a myopathic form of mitochondrial DNA depletion syndrome. Alternate splicing results in multiple transcript variants encoding distinct isoforms, some of which lack transit peptide, so are not localized to mitochondria. [provided by RefSeq, Dec 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TK2 | ENST00000569718.6 | c.-351-89G>C | intron_variant | 1 | |||||
TK2 | ENST00000678015.1 | c.-563G>C | 5_prime_UTR_variant | 1/10 | |||||
TK2 | ENST00000678297.1 | c.-488G>C | 5_prime_UTR_variant | 1/9 |
Frequencies
GnomAD3 genomes ? AF: 0.249 AC: 37886AN: 151998Hom.: 7192 Cov.: 33
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33
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GnomAD4 exome AF: 0.118 AC: 4AN: 34Hom.: 0 AF XY: 0.0625 AC XY: 1AN XY: 16
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GnomAD4 genome ? AF: 0.250 AC: 37957AN: 152116Hom.: 7212 Cov.: 33 AF XY: 0.248 AC XY: 18413AN XY: 74374
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at