17-78174869-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003258.5(TK1):c.595G>A(p.Gly199Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,613,696 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G199V) has been classified as Uncertain significance.
Frequency
Consequence
NM_003258.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TK1 | NM_003258.5 | c.595G>A | p.Gly199Arg | missense_variant | Exon 7 of 7 | ENST00000301634.12 | NP_003249.3 | |
TK1 | NM_001363848.1 | c.694G>A | p.Gly232Arg | missense_variant | Exon 6 of 6 | NP_001350777.1 | ||
TK1 | NM_001346663.2 | c.514-81G>A | intron_variant | Intron 6 of 6 | NP_001333592.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 247586Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134248
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461476Hom.: 0 Cov.: 33 AF XY: 0.0000303 AC XY: 22AN XY: 726994
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.595G>A (p.G199R) alteration is located in exon 7 (coding exon 7) of the TK1 gene. This alteration results from a G to A substitution at nucleotide position 595, causing the glycine (G) at amino acid position 199 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at