rs755544588
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4BP6_Moderate
The NM_004484.4(GPC3):c.1255G>A(p.Asp419Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000331 in 1,209,521 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D419G) has been classified as Uncertain significance.
Frequency
Consequence
NM_004484.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPC3 | NM_004484.4 | c.1255G>A | p.Asp419Asn | missense_variant | 5/8 | ENST00000370818.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPC3 | ENST00000370818.8 | c.1255G>A | p.Asp419Asn | missense_variant | 5/8 | 1 | NM_004484.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000885 AC: 1AN: 112994Hom.: 0 Cov.: 24 AF XY: 0.0000285 AC XY: 1AN XY: 35146
GnomAD3 exomes AF: 0.00000545 AC: 1AN: 183386Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67850
GnomAD4 exome AF: 0.00000274 AC: 3AN: 1096475Hom.: 0 Cov.: 29 AF XY: 0.00000276 AC XY: 1AN XY: 361867
GnomAD4 genome ? AF: 0.00000885 AC: 1AN: 113046Hom.: 0 Cov.: 24 AF XY: 0.0000284 AC XY: 1AN XY: 35208
ClinVar
Submissions by phenotype
Wilms tumor 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 10, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at