rs1965222
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000844.4(GRM7):c.1516-16915C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 456,316 control chromosomes in the GnomAD database, including 3,098 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 0.12 ( 1229 hom., cov: 32)
Exomes 𝑓: 0.10 ( 1869 hom. )
Consequence
GRM7
NM_000844.4 intron
NM_000844.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.114
Genes affected
GRM7 (HGNC:4599): (glutamate metabotropic receptor 7) L-glutamate is the major excitatory neurotransmitter in the central nervous system, and it activates both ionotropic and metabotropic glutamate receptors. Glutamatergic neurotransmission is involved in most aspects of normal brain function and can be perturbed in many neuropathologic conditions. The metabotropic glutamate receptors are a family of G protein-coupled receptors that have been divided into three groups on the basis of sequence homology, putative signal transduction mechanisms, and pharmacologic properties. Group I includes GRM1 and GRM5, and these receptors have been shown to activate phospholipase C. Group II includes GRM2 and GRM3, while Group III includes GRM4, GRM6, GRM7 and GRM8. Group II and III receptors are linked to the inhibition of the cyclic AMP cascade but differ in their agonist selectivities. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRM7 | NM_000844.4 | c.1516-16915C>T | intron_variant | ENST00000357716.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRM7 | ENST00000357716.9 | c.1516-16915C>T | intron_variant | 1 | NM_000844.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.123 AC: 18629AN: 151922Hom.: 1229 Cov.: 32
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GnomAD3 exomes AF: 0.0940 AC: 12618AN: 134250Hom.: 748 AF XY: 0.0895 AC XY: 6542AN XY: 73122
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GnomAD4 exome AF: 0.100 AC: 30421AN: 304276Hom.: 1869 Cov.: 0 AF XY: 0.0928 AC XY: 16084AN XY: 173254
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GnomAD4 genome ? AF: 0.123 AC: 18631AN: 152040Hom.: 1229 Cov.: 32 AF XY: 0.122 AC XY: 9055AN XY: 74360
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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