X-133953061-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4BP6_ModerateBS2
The NM_004484.4(GPC3):c.326C>T(p.Ala109Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,206,725 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A109E) 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 -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPC3 | NM_004484.4 | c.326C>T | p.Ala109Val | missense_variant | 2/8 | ENST00000370818.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPC3 | ENST00000370818.8 | c.326C>T | p.Ala109Val | missense_variant | 2/8 | 1 | NM_004484.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000448 AC: 5AN: 111671Hom.: 0 Cov.: 23 AF XY: 0.0000886 AC XY: 3AN XY: 33855
GnomAD3 exomes AF: 0.0000218 AC: 4AN: 183225Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67733
GnomAD4 exome AF: 0.0000119 AC: 13AN: 1095054Hom.: 0 Cov.: 29 AF XY: 0.00000832 AC XY: 3AN XY: 360576
GnomAD4 genome AF: 0.0000448 AC: 5AN: 111671Hom.: 0 Cov.: 23 AF XY: 0.0000886 AC XY: 3AN XY: 33855
ClinVar
Submissions by phenotype
Wilms tumor 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 23, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at