19-1105456-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_002085.5(GPX4):c.270C>T(p.Tyr90Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,612,568 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_002085.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPX4 | NM_002085.5 | c.270C>T | p.Tyr90Tyr | synonymous_variant | 3/7 | ENST00000354171.13 | NP_002076.2 | |
GPX4 | NM_001039848.4 | c.381C>T | p.Tyr127Tyr | synonymous_variant | 3/7 | NP_001034937.1 | ||
GPX4 | NM_001039847.3 | c.270C>T | p.Tyr90Tyr | synonymous_variant | 3/7 | NP_001034936.1 | ||
GPX4 | NM_001367832.1 | c.189C>T | p.Tyr63Tyr | synonymous_variant | 3/7 | NP_001354761.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 247842Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135098
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460364Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 726468
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74354
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at