rs727503064
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_133261.3(GIPC3):c.674G>A(p.Arg225His) variant causes a missense change. The variant allele was found at a frequency of 0.00000821 in 1,461,670 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R225C) has been classified as Uncertain significance.
Frequency
Consequence
NM_133261.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GIPC3 | NM_133261.3 | c.674G>A | p.Arg225His | missense_variant | 4/6 | ENST00000644452.3 | |
GIPC3 | NM_001411144.1 | c.674G>A | p.Arg225His | missense_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GIPC3 | ENST00000644452.3 | c.674G>A | p.Arg225His | missense_variant | 4/6 | NM_133261.3 | P1 | ||
GIPC3 | ENST00000644946.1 | c.674G>A | p.Arg225His | missense_variant | 4/6 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000800 AC: 2AN: 250068Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135600
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461670Hom.: 0 Cov.: 32 AF XY: 0.00000963 AC XY: 7AN XY: 727128
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Nov 10, 2014 | The p.Arg225His variant in GIPC3 has not been previously reported in individuals with hearing loss or in large population studies. Computational prediction tool s and conservation analysis suggest that this variant may impact the protein, th ough this information is not predictive enough to determine pathogenicity. In su mmary, the clinical significance of the p.Arg225His variant is uncertain. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at