chr10-5785253-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_001494.4(GDI2):āc.608A>Gā(p.Tyr203Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000414 in 1,450,144 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_001494.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GDI2 | NM_001494.4 | c.608A>G | p.Tyr203Cys | missense_variant | 6/11 | ENST00000380191.9 | |
GDI2 | NM_001115156.2 | c.473A>G | p.Tyr158Cys | missense_variant | 5/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GDI2 | ENST00000380191.9 | c.608A>G | p.Tyr203Cys | missense_variant | 6/11 | 1 | NM_001494.4 | P1 | |
GDI2 | ENST00000380181.7 | c.473A>G | p.Tyr158Cys | missense_variant | 5/10 | 1 | |||
GDI2 | ENST00000456041.5 | c.578A>G | p.Tyr193Cys | missense_variant | 6/7 | 5 | |||
GDI2 | ENST00000447751.5 | c.92A>G | p.Tyr31Cys | missense_variant | 2/6 | 3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250050Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135228
GnomAD4 exome AF: 0.00000414 AC: 6AN: 1450144Hom.: 0 Cov.: 26 AF XY: 0.00000415 AC XY: 3AN XY: 722072
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at