rs1129614
Positions:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001494.4(GDI2):c.1221C>T(p.Thr407=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 1,611,522 control chromosomes in the GnomAD database, including 32,951 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.17 ( 2457 hom., cov: 32)
Exomes 𝑓: 0.20 ( 30494 hom. )
Consequence
GDI2
NM_001494.4 synonymous
NM_001494.4 synonymous
Scores
2
13
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.106
Genes affected
GDI2 (HGNC:4227): (GDP dissociation inhibitor 2) GDP dissociation inhibitors are proteins that regulate the GDP-GTP exchange reaction of members of the rab family, small GTP-binding proteins of the ras superfamily, that are involved in vesicular trafficking of molecules between cellular organelles. GDIs slow the rate of dissociation of GDP from rab proteins and release GDP from membrane-bound rabs. GDI2 is ubiquitously expressed. The GDI2 gene contains many repetitive elements indicating that it may be prone to inversion/deletion rearrangements. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0017267466).
BP7
?
Synonymous conserved (PhyloP=-0.106 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GDI2 | NM_001494.4 | c.1221C>T | p.Thr407= | synonymous_variant | 11/11 | ENST00000380191.9 | |
GDI2 | NM_001115156.2 | c.1086C>T | p.Thr362= | synonymous_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GDI2 | ENST00000380191.9 | c.1221C>T | p.Thr407= | synonymous_variant | 11/11 | 1 | NM_001494.4 | P1 | |
GDI2 | ENST00000380181.7 | c.1086C>T | p.Thr362= | synonymous_variant | 10/10 | 1 | |||
GDI2 | ENST00000447751.5 | c.560C>T | p.Pro187Leu | missense_variant | 6/6 | 3 | |||
GDI2 | ENST00000479928.1 | n.1605C>T | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.169 AC: 25708AN: 152048Hom.: 2454 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.186 AC: 46723AN: 251142Hom.: 4775 AF XY: 0.185 AC XY: 25103AN XY: 135752
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GnomAD4 exome AF: 0.200 AC: 292219AN: 1459356Hom.: 30494 Cov.: 30 AF XY: 0.198 AC XY: 143663AN XY: 726118
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GnomAD4 genome ? AF: 0.169 AC: 25715AN: 152166Hom.: 2457 Cov.: 32 AF XY: 0.168 AC XY: 12491AN XY: 74384
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768
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813
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340
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22002
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
P;P;P
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
D
Sift4G
Uncertain
D
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at