17-78174847-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000301634.12(TK1):c.617G>T(p.Cys206Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,613,690 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 (★).
Frequency
Consequence
ENST00000301634.12 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TK1 | NM_003258.5 | c.617G>T | p.Cys206Phe | missense_variant | 7/7 | ENST00000301634.12 | NP_003249.3 | |
TK1 | NM_001363848.1 | c.716G>T | p.Cys239Phe | missense_variant | 6/6 | NP_001350777.1 | ||
TK1 | NM_001346663.2 | c.514-59G>T | intron_variant | NP_001333592.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TK1 | ENST00000301634.12 | c.617G>T | p.Cys206Phe | missense_variant | 7/7 | 1 | NM_003258.5 | ENSP00000301634 | P1 | |
TK1 | ENST00000588734.5 | c.716G>T | p.Cys239Phe | missense_variant | 6/6 | 2 | ENSP00000468425 | |||
TK1 | ENST00000590430.5 | c.*358G>T | 3_prime_UTR_variant | 5/5 | 3 | ENSP00000467121 | ||||
TK1 | ENST00000590862.5 | c.514-59G>T | intron_variant | 3 | ENSP00000468556 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152242Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000243 AC: 6AN: 247300Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134156
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461330Hom.: 0 Cov.: 33 AF XY: 0.00000550 AC XY: 4AN XY: 726914
GnomAD4 genome AF: 0.000125 AC: 19AN: 152360Hom.: 0 Cov.: 32 AF XY: 0.0000939 AC XY: 7AN XY: 74512
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 24, 2024 | The c.617G>T (p.C206F) alteration is located in exon 7 (coding exon 7) of the TK1 gene. This alteration results from a G to T substitution at nucleotide position 617, causing the cysteine (C) at amino acid position 206 to be replaced by a phenylalanine (F). 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