rs77358162
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM1PM2BP4
The NM_022445.4(TPK1):c.98G>T(p.Arg33Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,611,222 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R33H) has been classified as Likely benign.
Frequency
Consequence
NM_022445.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TPK1 | NM_022445.4 | c.98G>T | p.Arg33Leu | missense_variant | 3/9 | ENST00000360057.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TPK1 | ENST00000360057.7 | c.98G>T | p.Arg33Leu | missense_variant | 3/9 | 1 | NM_022445.4 | P1 | |
TPK1 | ENST00000378098.8 | c.98G>T | p.Arg33Leu | missense_variant, NMD_transcript_variant | 3/10 | 1 | |||
TPK1 | ENST00000378099.7 | c.98G>T | p.Arg33Leu | missense_variant | 3/8 | 3 | |||
TPK1 | ENST00000552881.1 | c.98G>T | p.Arg33Leu | missense_variant | 3/7 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151930Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1459292Hom.: 0 Cov.: 31 AF XY: 0.00000276 AC XY: 2AN XY: 725884
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151930Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74194
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at