rs17000463
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_004484.4(GPC3):c.1293-3501T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0135 in 111,930 control chromosomes in the GnomAD database, including 24 homozygotes. There are 411 hemizygotes in GnomAD. 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_004484.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPC3 | NM_004484.4 | c.1293-3501T>A | intron_variant | ENST00000370818.8 | |||
GPC3 | NM_001164617.2 | c.1362-3501T>A | intron_variant | ||||
GPC3 | NM_001164618.2 | c.1245-3501T>A | intron_variant | ||||
GPC3 | NM_001164619.2 | c.1131-3501T>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPC3 | ENST00000370818.8 | c.1293-3501T>A | intron_variant | 1 | NM_004484.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0134 AC: 1503AN: 111876Hom.: 24 Cov.: 23 AF XY: 0.0120 AC XY: 410AN XY: 34054
GnomAD4 genome AF: 0.0135 AC: 1509AN: 111930Hom.: 24 Cov.: 23 AF XY: 0.0120 AC XY: 411AN XY: 34118
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at