chr7-6503654-G-C
Position:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001145118.2(GRID2IP):c.2744C>G(p.Ala915Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Consequence
GRID2IP
NM_001145118.2 missense
NM_001145118.2 missense
Scores
1
17
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.02
Genes affected
GRID2IP (HGNC:18464): (Grid2 interacting protein) Glutamate receptor delta-2 (GRID2; MIM 602368) is predominantly expressed at parallel fiber-Purkinje cell postsynapses and plays crucial roles in synaptogenesis and synaptic plasticity. GRID2IP1 interacts with GRID2 and may control GRID2 signaling in Purkinje cells (Matsuda et al., 2006 [PubMed 16835239]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.032257736).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRID2IP | NM_001145118.2 | c.2744C>G | p.Ala915Gly | missense_variant | 16/22 | ENST00000457091.3 | |
GRID2IP | NM_001394781.1 | c.2195C>G | p.Ala732Gly | missense_variant | 15/21 | ||
GRID2IP | NM_001388403.1 | c.2171C>G | p.Ala724Gly | missense_variant | 15/21 | ||
GRID2IP | XM_047420365.1 | c.2174C>G | p.Ala725Gly | missense_variant | 15/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRID2IP | ENST00000457091.3 | c.2744C>G | p.Ala915Gly | missense_variant | 16/22 | 5 | NM_001145118.2 | P1 | |
GRID2IP | ENST00000435185.5 | c.2192C>G | p.Ala731Gly | missense_variant | 15/21 | 5 | |||
GRID2IP | ENST00000452113.5 | c.2171C>G | p.Ala724Gly | missense_variant | 15/21 | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Cov.: 34
GnomAD4 exome
Cov.:
34
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;.;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T
M_CAP
Benign
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
0.0
.;.;B
Vest4
MutPred
0.35
.;.;Gain of methylation at K911 (P = 0.0986);
MVP
MPC
0.21
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.