chr19-1104053-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002085.5(GPX4):c.10G>T(p.Gly4Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000494 in 1,519,608 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002085.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPX4 | NM_002085.5 | c.10G>T | p.Gly4Cys | missense_variant | 1/7 | ENST00000354171.13 | NP_002076.2 | |
GPX4 | NM_001039847.3 | c.10G>T | p.Gly4Cys | missense_variant | 1/7 | NP_001034936.1 | ||
GPX4 | NM_001367832.1 | upstream_gene_variant | NP_001354761.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPX4 | ENST00000354171.13 | c.10G>T | p.Gly4Cys | missense_variant | 1/7 | 1 | NM_002085.5 | ENSP00000346103 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152254Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000344 AC: 4AN: 116112Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 64316
GnomAD4 exome AF: 0.0000461 AC: 63AN: 1367354Hom.: 0 Cov.: 30 AF XY: 0.0000430 AC XY: 29AN XY: 674556
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152254Hom.: 0 Cov.: 34 AF XY: 0.0000672 AC XY: 5AN XY: 74382
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 19, 2022 | The c.10G>T (p.G4C) alteration is located in exon 1 (coding exon 1) of the GPX4 gene. This alteration results from a G to T substitution at nucleotide position 10, causing the glycine (G) at amino acid position 4 to be replaced by a cysteine (C). 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