chr3-49357401-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000581.4(GPX1):c.599C>T(p.Pro200Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 1,607,594 control chromosomes in the GnomAD database, including 76,163 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000581.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPX1 | NM_000581.4 | c.599C>T | p.Pro200Leu | missense_variant | 2/2 | ENST00000419783.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPX1 | ENST00000419783.3 | c.599C>T | p.Pro200Leu | missense_variant | 2/2 | 1 | NM_000581.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.297 AC: 45043AN: 151596Hom.: 7165 Cov.: 30
GnomAD3 exomes AF: 0.280 AC: 68269AN: 244032Hom.: 11117 AF XY: 0.283 AC XY: 37740AN XY: 133308
GnomAD4 exome AF: 0.300 AC: 436513AN: 1455880Hom.: 68991 Cov.: 34 AF XY: 0.299 AC XY: 215897AN XY: 723240
GnomAD4 genome ? AF: 0.297 AC: 45072AN: 151714Hom.: 7172 Cov.: 30 AF XY: 0.299 AC XY: 22165AN XY: 74098
ClinVar
Submissions by phenotype
GLUTATHIONE PEROXIDASE POLYMORPHISM Benign:1
Benign, no assertion criteria provided | literature only | OMIM | Jan 01, 1999 | - - |
Gluthathione peroxidase deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Aug 16, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | This variant is associated with the following publications: (PMID: 27592002, 30256368, 22139612, 21636625, 18563616, 29411539, 11103801, 19826042, 22888637, 20178852, 21165435, 16287877, 20441054, 16956821, 21993316, 19415410, 23073788, 15331559, 16945136, 25047527) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at