rs8113232
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_133261.3(GIPC3):c.276G>A(p.Leu92Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 1,613,494 control chromosomes in the GnomAD database, including 23,097 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_133261.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GIPC3 | ENST00000644452.3 | c.276G>A | p.Leu92Leu | synonymous_variant | Exon 2 of 6 | NM_133261.3 | ENSP00000493901.2 | |||
GIPC3 | ENST00000644946.1 | c.276G>A | p.Leu92Leu | synonymous_variant | Exon 2 of 6 | ENSP00000495068.1 |
Frequencies
GnomAD3 genomes AF: 0.229 AC: 34745AN: 151990Hom.: 6432 Cov.: 31
GnomAD3 exomes AF: 0.137 AC: 34256AN: 250884Hom.: 3916 AF XY: 0.130 AC XY: 17681AN XY: 135786
GnomAD4 exome AF: 0.133 AC: 194965AN: 1461386Hom.: 16638 Cov.: 39 AF XY: 0.132 AC XY: 95623AN XY: 727008
GnomAD4 genome AF: 0.229 AC: 34820AN: 152108Hom.: 6459 Cov.: 31 AF XY: 0.222 AC XY: 16520AN XY: 74366
ClinVar
Submissions by phenotype
not specified Benign:4
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Leu92Leu in Exon 02 of GIPC3: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue, is not located within the splice consensus sequence, and has been identified in 48.7% (1820/3738) of African American chromosomes from a broad population by the NHLBI Exome Sequenci ng Project (http://evs.gs.washington.edu/EVS; dbSNP rs8113232). -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at