22-50526648-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP3_StrongPP5
The NM_001953.5(TYMP):c.856G>A(p.Glu286Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00000639 in 1,565,024 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. E286E) has been classified as Likely benign.
Frequency
Consequence
NM_001953.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TYMP | NM_001953.5 | c.856G>A | p.Glu286Lys | missense_variant | 7/10 | ENST00000252029.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TYMP | ENST00000252029.8 | c.856G>A | p.Glu286Lys | missense_variant | 7/10 | 1 | NM_001953.5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152268Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000425 AC: 6AN: 1412756Hom.: 0 Cov.: 36 AF XY: 0.00000286 AC XY: 2AN XY: 698802
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152268Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74392
ClinVar
Submissions by phenotype
Mitochondrial DNA depletion syndrome 1 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | GeneReviews | Jan 14, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at