1-52608346-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015696.5(GPX7):c.485C>T(p.Thr162Ile) variant causes a missense change. The variant allele was found at a frequency of 0.000107 in 1,613,996 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015696.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPX7 | NM_015696.5 | c.485C>T | p.Thr162Ile | missense_variant | Exon 3 of 3 | ENST00000361314.5 | NP_056511.2 | |
GPX7 | XM_047418560.1 | c.377C>T | p.Thr126Ile | missense_variant | Exon 3 of 3 | XP_047274516.1 | ||
GPX7 | XM_047418564.1 | c.356C>T | p.Thr119Ile | missense_variant | Exon 3 of 3 | XP_047274520.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251386Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135858
GnomAD4 exome AF: 0.000112 AC: 164AN: 1461816Hom.: 0 Cov.: 30 AF XY: 0.000116 AC XY: 84AN XY: 727224
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.485C>T (p.T162I) alteration is located in exon 3 (coding exon 3) of the GPX7 gene. This alteration results from a C to T substitution at nucleotide position 485, causing the threonine (T) at amino acid position 162 to be replaced by an isoleucine (I). 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