chr6-28534102-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001509.3(GPX5):c.601C>T(p.Arg201Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000614 in 1,611,258 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001509.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPX5 | NM_001509.3 | c.601C>T | p.Arg201Trp | missense_variant | Exon 5 of 5 | ENST00000412168.7 | NP_001500.1 | |
GPX5 | NM_003996.3 | c.*180C>T | 3_prime_UTR_variant | Exon 4 of 4 | NP_003987.2 | |||
GPX5 | NR_144470.2 | n.679C>T | non_coding_transcript_exon_variant | Exon 4 of 4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPX5 | ENST00000412168.7 | c.601C>T | p.Arg201Trp | missense_variant | Exon 5 of 5 | 1 | NM_001509.3 | ENSP00000392398.2 | ||
GPX5 | ENST00000442674.6 | n.976C>T | non_coding_transcript_exon_variant | Exon 6 of 6 | 5 | |||||
GPX5 | ENST00000469384.1 | c.*180C>T | downstream_gene_variant | 1 | ENSP00000419935.1 | |||||
GPX5 | ENST00000483784.1 | n.*123C>T | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000921 AC: 14AN: 152010Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000766 AC: 19AN: 248200Hom.: 0 AF XY: 0.0000670 AC XY: 9AN XY: 134252
GnomAD4 exome AF: 0.0000582 AC: 85AN: 1459248Hom.: 1 Cov.: 31 AF XY: 0.0000647 AC XY: 47AN XY: 725950
GnomAD4 genome AF: 0.0000921 AC: 14AN: 152010Hom.: 0 Cov.: 32 AF XY: 0.0000943 AC XY: 7AN XY: 74250
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.601C>T (p.R201W) alteration is located in exon 5 (coding exon 5) of the GPX5 gene. This alteration results from a C to T substitution at nucleotide position 601, causing the arginine (R) at amino acid position 201 to be replaced by a tryptophan (W). 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