NM_004484.4:c.569C>T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_004484.4(GPC3):c.569C>T(p.Ser190Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000331 in 1,209,056 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_004484.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000179 AC: 2AN: 111934Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 34104
GnomAD3 exomes AF: 0.0000164 AC: 3AN: 182455Hom.: 0 AF XY: 0.0000446 AC XY: 3AN XY: 67335
GnomAD4 exome AF: 0.00000182 AC: 2AN: 1097122Hom.: 0 Cov.: 32 AF XY: 0.00000276 AC XY: 1AN XY: 362500
GnomAD4 genome AF: 0.0000179 AC: 2AN: 111934Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 34104
ClinVar
Submissions by phenotype
GPC3-related disorder Uncertain:1
The GPC3 c.569C>T variant is predicted to result in the amino acid substitution p.Ser190Leu. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.023% of alleles in individuals of African descent in gnomAD, including three hemizygous individuals (http://gnomad.broadinstitute.org/variant/X-132887972-G-A) and is reported by one outside laboratory as likely benign in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/543085/). Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Wilms tumor 1 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at