rs8177447
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002084.5(GPX3):c.460-14T>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,458,108 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_002084.5 splice_polypyrimidine_tract, intron
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 |
---|---|---|---|---|---|---|---|
GPX3 | NM_002084.5 | c.460-14T>A | splice_polypyrimidine_tract_variant, intron_variant | ENST00000388825.9 | |||
GPX3 | NM_001329790.2 | c.487-14T>A | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPX3 | ENST00000388825.9 | c.460-14T>A | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_002084.5 | P1 | |||
GPX3 | ENST00000520059.1 | c.227T>A | p.Leu76Ter | stop_gained | 3/3 | 3 | |||
GPX3 | ENST00000517973.1 | c.*3-14T>A | splice_polypyrimidine_tract_variant, intron_variant | 3 | |||||
GPX3 | ENST00000521632.1 | c.269-14T>A | splice_polypyrimidine_tract_variant, intron_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249148Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135214
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1458108Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 725680
GnomAD4 genome ? Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at