rs373406834
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_004484.4(GPC3):c.672A>G(p.Gln224=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000091 in 1,209,418 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. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_004484.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPC3 | NM_004484.4 | c.672A>G | p.Gln224= | synonymous_variant | 3/8 | ENST00000370818.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPC3 | ENST00000370818.8 | c.672A>G | p.Gln224= | synonymous_variant | 3/8 | 1 | NM_004484.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000447 AC: 5AN: 111953Hom.: 0 Cov.: 23 AF XY: 0.0000880 AC XY: 3AN XY: 34107
GnomAD3 exomes AF: 0.0000220 AC: 4AN: 182073Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67311
GnomAD4 exome AF: 0.00000547 AC: 6AN: 1097465Hom.: 0 Cov.: 33 AF XY: 0.00000276 AC XY: 1AN XY: 362831
GnomAD4 genome ? AF: 0.0000447 AC: 5AN: 111953Hom.: 0 Cov.: 23 AF XY: 0.0000880 AC XY: 3AN XY: 34107
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | curation | Sema4, Sema4 | Feb 10, 2022 | - - |
Wilms tumor 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 17, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at