chr6-28531811-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001509.3(GPX5):āc.275A>Gā(p.Tyr92Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000135 in 1,613,236 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y92D) has been classified as Uncertain significance.
Frequency
Consequence
NM_001509.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPX5 | NM_001509.3 | c.275A>G | p.Tyr92Cys | missense_variant | 3/5 | ENST00000412168.7 | |
GPX5 | NM_003996.3 | c.242-510A>G | intron_variant | ||||
GPX5 | NR_144470.2 | n.438-510A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPX5 | ENST00000412168.7 | c.275A>G | p.Tyr92Cys | missense_variant | 3/5 | 1 | NM_001509.3 | P1 | |
GPX5 | ENST00000469384.1 | c.242-510A>G | intron_variant | 1 | |||||
GPX5 | ENST00000442674.6 | n.650A>G | non_coding_transcript_exon_variant | 4/6 | 5 | ||||
GPX5 | ENST00000483784.1 | n.433-510A>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000439 AC: 11AN: 250780Hom.: 0 AF XY: 0.0000664 AC XY: 9AN XY: 135528
GnomAD4 exome AF: 0.000145 AC: 212AN: 1461116Hom.: 0 Cov.: 30 AF XY: 0.000139 AC XY: 101AN XY: 726870
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152120Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 30, 2024 | The c.275A>G (p.Y92C) alteration is located in exon 3 (coding exon 3) of the GPX5 gene. This alteration results from a A to G substitution at nucleotide position 275, causing the tyrosine (Y) at amino acid position 92 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