rs148951753
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4BP6_Very_StrongBS2
The ENST00000370818.8(GPC3):āc.889A>Gā(p.Arg297Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000266 in 1,209,352 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 95 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R297K) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000370818.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPC3 | NM_004484.4 | c.889A>G | p.Arg297Gly | missense_variant | 3/8 | ENST00000370818.8 | NP_004475.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPC3 | ENST00000370818.8 | c.889A>G | p.Arg297Gly | missense_variant | 3/8 | 1 | NM_004484.4 | ENSP00000359854 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000187 AC: 21AN: 112223Hom.: 0 Cov.: 23 AF XY: 0.000145 AC XY: 5AN XY: 34377
GnomAD3 exomes AF: 0.000207 AC: 38AN: 183321Hom.: 0 AF XY: 0.000133 AC XY: 9AN XY: 67811
GnomAD4 exome AF: 0.000274 AC: 301AN: 1097076Hom.: 0 Cov.: 32 AF XY: 0.000248 AC XY: 90AN XY: 362454
GnomAD4 genome AF: 0.000187 AC: 21AN: 112276Hom.: 0 Cov.: 23 AF XY: 0.000145 AC XY: 5AN XY: 34440
ClinVar
Submissions by phenotype
not provided Benign:4
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 02, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2023 | GPC3: BP4, BS2 - |
Wilms tumor 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 09, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at