chrX-133753753-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_004484.4(GPC3):c.761G>T(p.Arg254Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000237 in 1,097,750 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 14 hemizygotes in GnomAD. 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. R254Q) has been classified as Likely benign.
Frequency
Consequence
NM_004484.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPC3 | NM_004484.4 | c.761G>T | p.Arg254Leu | missense_variant | 3/8 | ENST00000370818.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPC3 | ENST00000370818.8 | c.761G>T | p.Arg254Leu | missense_variant | 3/8 | 1 | NM_004484.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 111964Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34124 FAILED QC
GnomAD3 exomes AF: 0.0000328 AC: 6AN: 182851Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67489
GnomAD4 exome AF: 0.0000237 AC: 26AN: 1097750Hom.: 0 Cov.: 33 AF XY: 0.0000386 AC XY: 14AN XY: 363114
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 111964Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34124
ClinVar
Submissions by phenotype
Wilms tumor 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 18, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at