chr10-5766140-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001494.4(GDI2):c.1204C>T(p.Arg402Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000806 in 1,613,402 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 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. R402H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001494.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GDI2 | NM_001494.4 | c.1204C>T | p.Arg402Cys | missense_variant | 11/11 | ENST00000380191.9 | |
GDI2 | NM_001115156.2 | c.1069C>T | p.Arg357Cys | missense_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GDI2 | ENST00000380191.9 | c.1204C>T | p.Arg402Cys | missense_variant | 11/11 | 1 | NM_001494.4 | P1 | |
GDI2 | ENST00000380181.7 | c.1069C>T | p.Arg357Cys | missense_variant | 10/10 | 1 | |||
GDI2 | ENST00000447751.5 | c.543C>T | p.Pro181= | synonymous_variant | 6/6 | 3 | |||
GDI2 | ENST00000479928.1 | n.1588C>T | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152094Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251290Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135814
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461308Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 727006
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152094Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74290
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 26, 2023 | The c.1204C>T (p.R402C) alteration is located in exon 11 (coding exon 11) of the GDI2 gene. This alteration results from a C to T substitution at nucleotide position 1204, causing the arginine (R) at amino acid position 402 to be replaced by a cysteine (C). 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