rs1800202
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The ENST00000229270.8(TPI1):c.50T>A(p.Ile17Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000127 in 1,579,216 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/17 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. I17R) has been classified as Likely benign.
Frequency
Consequence
ENST00000229270.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TPI1 | NM_001159287.1 | c.50T>A | p.Ile17Lys | missense_variant | 1/7 | ||
TPI1 | NM_000365.6 | upstream_gene_variant | ENST00000396705.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TPI1 | ENST00000229270.8 | c.50T>A | p.Ile17Lys | missense_variant | 1/7 | 1 | |||
TPI1 | ENST00000613953.4 | c.50T>A | p.Ile17Lys | missense_variant | 1/7 | 1 | |||
TPI1 | ENST00000396705.10 | upstream_gene_variant | 1 | NM_000365.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151968Hom.: 0 Cov.: 34
GnomAD4 exome AF: 7.01e-7 AC: 1AN: 1427248Hom.: 0 Cov.: 34 AF XY: 0.00000141 AC XY: 1AN XY: 707182
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151968Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74218
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at