rs745317547
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP6_Moderate
The NM_004484.4(GPC3):c.584A>G(p.Asn195Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000909 in 1,209,584 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict 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. N195D) 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 -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPC3 | NM_004484.4 | c.584A>G | p.Asn195Ser | missense_variant | 3/8 | ENST00000370818.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPC3 | ENST00000370818.8 | c.584A>G | p.Asn195Ser | missense_variant | 3/8 | 1 | NM_004484.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000894 AC: 1AN: 111808Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33990
GnomAD3 exomes AF: 0.0000165 AC: 3AN: 182370Hom.: 0 AF XY: 0.0000149 AC XY: 1AN XY: 67310
GnomAD4 exome AF: 0.00000911 AC: 10AN: 1097776Hom.: 0 Cov.: 33 AF XY: 0.0000110 AC XY: 4AN XY: 363144
GnomAD4 genome ? AF: 0.00000894 AC: 1AN: 111808Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33990
ClinVar
Submissions by phenotype
Wilms tumor 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 02, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at