rs745968470
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6BP7BS2
The NM_004484.4(GPC3):c.1398G>A(p.Leu466=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000274 in 1,167,550 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 13 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_004484.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPC3 | NM_004484.4 | c.1398G>A | p.Leu466= | synonymous_variant | 6/8 | ENST00000370818.8 | |
GPC3 | NM_001164617.2 | c.1467G>A | p.Leu489= | synonymous_variant | 7/9 | ||
GPC3 | NM_001164618.2 | c.1350G>A | p.Leu450= | synonymous_variant | 6/8 | ||
GPC3 | NM_001164619.2 | c.1236G>A | p.Leu412= | synonymous_variant | 5/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPC3 | ENST00000370818.8 | c.1398G>A | p.Leu466= | synonymous_variant | 6/8 | 1 | NM_004484.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000287 AC: 3AN: 104611Hom.: 0 Cov.: 19 AF XY: 0.0000727 AC XY: 2AN XY: 27511
GnomAD3 exomes AF: 0.0000164 AC: 3AN: 183046Hom.: 0 AF XY: 0.0000296 AC XY: 2AN XY: 67528
GnomAD4 exome AF: 0.0000273 AC: 29AN: 1062939Hom.: 0 Cov.: 26 AF XY: 0.0000329 AC XY: 11AN XY: 334147
GnomAD4 genome AF: 0.0000287 AC: 3AN: 104611Hom.: 0 Cov.: 19 AF XY: 0.0000727 AC XY: 2AN XY: 27511
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Mar 04, 2015 | - - |
Wilms tumor 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at