7-6502092-C-T
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001145118.2(GRID2IP):c.3177G>A(p.Gly1059=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000735 in 1,551,248 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.000066 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000074 ( 0 hom. )
Consequence
GRID2IP
NM_001145118.2 synonymous
NM_001145118.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.590
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 -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BP6
Variant 7-6502092-C-T is Benign according to our data. Variant chr7-6502092-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 731756.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.59 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRID2IP | NM_001145118.2 | c.3177G>A | p.Gly1059= | synonymous_variant | 19/22 | ENST00000457091.3 | |
GRID2IP | NM_001394781.1 | c.2628G>A | p.Gly876= | synonymous_variant | 18/21 | ||
GRID2IP | NM_001388403.1 | c.2604G>A | p.Gly868= | synonymous_variant | 18/21 | ||
GRID2IP | XM_047420365.1 | c.2607G>A | p.Gly869= | synonymous_variant | 18/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRID2IP | ENST00000457091.3 | c.3177G>A | p.Gly1059= | synonymous_variant | 19/22 | 5 | NM_001145118.2 | P1 | |
GRID2IP | ENST00000435185.5 | c.2625G>A | p.Gly875= | synonymous_variant | 18/21 | 5 | |||
GRID2IP | ENST00000452113.5 | c.2604G>A | p.Gly868= | synonymous_variant | 18/21 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000658 AC: 10AN: 152042Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000383 AC: 6AN: 156496Hom.: 0 AF XY: 0.0000482 AC XY: 4AN XY: 82942
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GnomAD4 exome AF: 0.0000743 AC: 104AN: 1399206Hom.: 0 Cov.: 32 AF XY: 0.0000667 AC XY: 46AN XY: 690112
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GnomAD4 genome AF: 0.0000658 AC: 10AN: 152042Hom.: 0 Cov.: 31 AF XY: 0.0000539 AC XY: 4AN XY: 74260
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 11, 2018 | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at