rs373916851
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_004484.4(GPC3):c.1037G>T(p.Gly346Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,185,211 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G346S) has been classified as Uncertain significance.
Frequency
Consequence
NM_004484.4 missense
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.1037G>T | p.Gly346Val | missense_variant | 4/8 | ENST00000370818.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPC3 | ENST00000370818.8 | c.1037G>T | p.Gly346Val | missense_variant | 4/8 | 1 | NM_004484.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000179 AC: 2AN: 111768Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33990
GnomAD3 exomes AF: 0.0000166 AC: 3AN: 180865Hom.: 0 AF XY: 0.0000152 AC XY: 1AN XY: 65629
GnomAD4 exome AF: 0.0000140 AC: 15AN: 1073443Hom.: 0 Cov.: 24 AF XY: 0.00000879 AC XY: 3AN XY: 341393
GnomAD4 genome ? AF: 0.0000179 AC: 2AN: 111768Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33990
ClinVar
Submissions by phenotype
Wilms tumor 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 26, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at