chr10-5773898-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001494.4(GDI2):c.763A>G(p.Ile255Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000293 in 1,567,826 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
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.763A>G | p.Ile255Val | missense_variant | 7/11 | ENST00000380191.9 | |
GDI2 | NM_001115156.2 | c.628A>G | p.Ile210Val | missense_variant | 6/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GDI2 | ENST00000380191.9 | c.763A>G | p.Ile255Val | missense_variant | 7/11 | 1 | NM_001494.4 | P1 | |
GDI2 | ENST00000380181.7 | c.628A>G | p.Ile210Val | missense_variant | 6/10 | 1 | |||
GDI2 | ENST00000456041.5 | c.733A>G | p.Ile245Val | missense_variant | 7/7 | 5 | |||
GDI2 | ENST00000447751.5 | c.247A>G | p.Ile83Val | missense_variant | 3/6 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 152230Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000570 AC: 14AN: 245824Hom.: 0 AF XY: 0.0000527 AC XY: 7AN XY: 132844
GnomAD4 exome AF: 0.0000177 AC: 25AN: 1415596Hom.: 0 Cov.: 24 AF XY: 0.0000127 AC XY: 9AN XY: 706576
GnomAD4 genome ? AF: 0.000138 AC: 21AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.000229 AC XY: 17AN XY: 74382
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 31, 2023 | The c.763A>G (p.I255V) alteration is located in exon 7 (coding exon 7) of the GDI2 gene. This alteration results from a A to G substitution at nucleotide position 763, causing the isoleucine (I) at amino acid position 255 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at